Tripal: a construction toolkit for online genome databases
Identifieur interne : 000520 ( Pmc/Curation ); précédent : 000519; suivant : 000521Tripal: a construction toolkit for online genome databases
Auteurs : Stephen P. Ficklin ; Lacey-Anne Sanderson [Canada] ; Chun-Huai Cheng ; Margaret E. Staton ; Taein Lee ; Il-Hyung Cho ; Sook Jung ; Kirstin E. Bett [Canada] ; Doreen MainSource :
- Database: The Journal of Biological Databases and Curation [ 1758-0463 ] ; 2011.
Abstract
As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at
Url:
DOI: 10.1093/database/bar044
PubMed: 21959868
PubMed Central: 3263599
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: Pour aller vers cette notice dans l'étape Curation :000520
Links to Exploration step
PMC:3263599Curation
No country items
Stephen P. Ficklin<affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation><affiliation><nlm:aff wicri:cut=" and" id="bar044-AFF1">Clemson University Genomics Institute (CUGI), Clemson University, Clemson, SC, USA 29634</nlm:aff><wicri:noCountry code="subfield">USA 29634</wicri:noCountry></affiliation><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation><affiliation><nlm:aff id="bar044-AFF1">Department of Computer Science, Saginaw Valley State University, University Center, MI, USA 48710</nlm:aff><wicri:noCountry code="subfield">USA 48710</wicri:noCountry></affiliation><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation>Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Tripal: a construction toolkit for online genome databases</title><author><name sortKey="Ficklin, Stephen P" sort="Ficklin, Stephen P" uniqKey="Ficklin S" first="Stephen P." last="Ficklin">Stephen P. Ficklin</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Sanderson, Lacey Anne" sort="Sanderson, Lacey Anne" uniqKey="Sanderson L" first="Lacey-Anne" last="Sanderson">Lacey-Anne Sanderson</name><affiliation wicri:level="1"><nlm:aff id="bar044-AFF1">Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada S7N 5B5,</nlm:aff><country>Canada</country><wicri:regionArea>Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK</wicri:regionArea></affiliation></author><author><name sortKey="Cheng, Chun Huai" sort="Cheng, Chun Huai" uniqKey="Cheng C" first="Chun-Huai" last="Cheng">Chun-Huai Cheng</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Staton, Margaret E" sort="Staton, Margaret E" uniqKey="Staton M" first="Margaret E." last="Staton">Margaret E. Staton</name><affiliation><nlm:aff wicri:cut=" and" id="bar044-AFF1">Clemson University Genomics Institute (CUGI), Clemson University, Clemson, SC, USA 29634</nlm:aff><wicri:noCountry code="subfield">USA 29634</wicri:noCountry></affiliation></author><author><name sortKey="Lee, Taein" sort="Lee, Taein" uniqKey="Lee T" first="Taein" last="Lee">Taein Lee</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Cho, Il Hyung" sort="Cho, Il Hyung" uniqKey="Cho I" first="Il-Hyung" last="Cho">Il-Hyung Cho</name><affiliation><nlm:aff id="bar044-AFF1">Department of Computer Science, Saginaw Valley State University, University Center, MI, USA 48710</nlm:aff><wicri:noCountry code="subfield">USA 48710</wicri:noCountry></affiliation></author><author><name sortKey="Jung, Sook" sort="Jung, Sook" uniqKey="Jung S" first="Sook" last="Jung">Sook Jung</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Bett, Kirstin E" sort="Bett, Kirstin E" uniqKey="Bett K" first="Kirstin E." last="Bett">Kirstin E. Bett</name><affiliation wicri:level="1"><nlm:aff id="bar044-AFF1">Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada S7N 5B5,</nlm:aff><country>Canada</country><wicri:regionArea>Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK</wicri:regionArea></affiliation></author><author><name sortKey="Main, Doreen" sort="Main, Doreen" uniqKey="Main D" first="Doreen" last="Main">Doreen Main</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21959868</idno><idno type="pmc">3263599</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263599</idno><idno type="RBID">PMC:3263599</idno><idno type="doi">10.1093/database/bar044</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000520</idno><idno type="wicri:Area/Pmc/Curation">000520</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Tripal: a construction toolkit for online genome databases</title><author><name sortKey="Ficklin, Stephen P" sort="Ficklin, Stephen P" uniqKey="Ficklin S" first="Stephen P." last="Ficklin">Stephen P. Ficklin</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Sanderson, Lacey Anne" sort="Sanderson, Lacey Anne" uniqKey="Sanderson L" first="Lacey-Anne" last="Sanderson">Lacey-Anne Sanderson</name><affiliation wicri:level="1"><nlm:aff id="bar044-AFF1">Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada S7N 5B5,</nlm:aff><country>Canada</country><wicri:regionArea>Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK</wicri:regionArea></affiliation></author><author><name sortKey="Cheng, Chun Huai" sort="Cheng, Chun Huai" uniqKey="Cheng C" first="Chun-Huai" last="Cheng">Chun-Huai Cheng</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Staton, Margaret E" sort="Staton, Margaret E" uniqKey="Staton M" first="Margaret E." last="Staton">Margaret E. Staton</name><affiliation><nlm:aff wicri:cut=" and" id="bar044-AFF1">Clemson University Genomics Institute (CUGI), Clemson University, Clemson, SC, USA 29634</nlm:aff><wicri:noCountry code="subfield">USA 29634</wicri:noCountry></affiliation></author><author><name sortKey="Lee, Taein" sort="Lee, Taein" uniqKey="Lee T" first="Taein" last="Lee">Taein Lee</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Cho, Il Hyung" sort="Cho, Il Hyung" uniqKey="Cho I" first="Il-Hyung" last="Cho">Il-Hyung Cho</name><affiliation><nlm:aff id="bar044-AFF1">Department of Computer Science, Saginaw Valley State University, University Center, MI, USA 48710</nlm:aff><wicri:noCountry code="subfield">USA 48710</wicri:noCountry></affiliation></author><author><name sortKey="Jung, Sook" sort="Jung, Sook" uniqKey="Jung S" first="Sook" last="Jung">Sook Jung</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author><author><name sortKey="Bett, Kirstin E" sort="Bett, Kirstin E" uniqKey="Bett K" first="Kirstin E." last="Bett">Kirstin E. Bett</name><affiliation wicri:level="1"><nlm:aff id="bar044-AFF1">Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada S7N 5B5,</nlm:aff><country>Canada</country><wicri:regionArea>Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK</wicri:regionArea></affiliation></author><author><name sortKey="Main, Doreen" sort="Main, Doreen" uniqKey="Main D" first="Doreen" last="Main">Doreen Main</name><affiliation><nlm:aff id="bar044-AFF1">Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,</nlm:aff><wicri:noCountry code="subfield">USA 99164</wicri:noCountry></affiliation></author></analytic><series><title level="j">Database: The Journal of Biological Databases and Curation</title><idno type="eISSN">1758-0463</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at <ext-link ext-link-type="uri" xlink:href="http://tripal.sourceforge.net">http://tripal.sourceforge.net</ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Drysdale, R" uniqKey="Drysdale R">R Drysdale</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Harris, Tw" uniqKey="Harris T">TW Harris</name></author><author><name sortKey="Antoshechkin, I" uniqKey="Antoshechkin I">I Antoshechkin</name></author><author><name sortKey="Bieri, T" uniqKey="Bieri T">T Bieri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hirschman, Je" uniqKey="Hirschman J">JE Hirschman</name></author><author><name sortKey="Engel, S" uniqKey="Engel S">S Engel</name></author><author><name sortKey="Hong, E" uniqKey="Hong E">E Hong</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jung, S" uniqKey="Jung S">S Jung</name></author><author><name sortKey="Staton, M" uniqKey="Staton M">M Staton</name></author><author><name sortKey="Lee, T" uniqKey="Lee T">T Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jung, S" uniqKey="Jung S">S Jung</name></author><author><name sortKey="Jesudurai, C" uniqKey="Jesudurai C">C Jesudurai</name></author><author><name sortKey="Staton, M" uniqKey="Staton M">M Staton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mckillen, Dj" uniqKey="Mckillen D">DJ McKillen</name></author><author><name sortKey="Chen, Ya" uniqKey="Chen Y">YA Chen</name></author><author><name sortKey="Chen, C" uniqKey="Chen C">C Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jaiswal, P" uniqKey="Jaiswal P">P Jaiswal</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lawrence, Cj" uniqKey="Lawrence C">CJ Lawrence</name></author><author><name sortKey="Dong, Q" uniqKey="Dong Q">Q Dong</name></author><author><name sortKey="Polacco, Ml" uniqKey="Polacco M">ML Polacco</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lawrence, Cj" uniqKey="Lawrence C">CJ Lawrence</name></author><author><name sortKey="Harper, Lc" uniqKey="Harper L">LC Harper</name></author><author><name sortKey="Schaeffer, Ml" uniqKey="Schaeffer M">ML Schaeffer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wegrzyn, Jl" uniqKey="Wegrzyn J">JL Wegrzyn</name></author><author><name sortKey="Lee, Jm" uniqKey="Lee J">JM Lee</name></author><author><name sortKey="Tearse, Br" uniqKey="Tearse B">BR Tearse</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bombarely, A" uniqKey="Bombarely A">A Bombarely</name></author><author><name sortKey="Menda, N" uniqKey="Menda N">N Menda</name></author><author><name sortKey="Tecle, Iy" uniqKey="Tecle I">IY Tecle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mungall, Cj" uniqKey="Mungall C">CJ Mungall</name></author><author><name sortKey="Emmert, Db" uniqKey="Emmert D">DB Emmert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, P" uniqKey="Zhou P">P Zhou</name></author><author><name sortKey="Emmert, D" uniqKey="Emmert D">D Emmert</name></author><author><name sortKey="Zhang, P" uniqKey="Zhang P">P Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Donlin, Mj" uniqKey="Donlin M">MJ Donlin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stein, Ld" uniqKey="Stein L">LD Stein</name></author><author><name sortKey="Mungall, C" uniqKey="Mungall C">C Mungall</name></author><author><name sortKey="Shu, Sq" uniqKey="Shu S">SQ Shu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lewis, Se" uniqKey="Lewis S">SE Lewis</name></author><author><name sortKey="Searle, Sm" uniqKey="Searle S">SM Searle</name></author><author><name sortKey="Harris, N" uniqKey="Harris N">N Harris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Orvis, J" uniqKey="Orvis J">J Orvis</name></author><author><name sortKey="Crabtree, J" uniqKey="Crabtree J">J Crabtree</name></author><author><name sortKey="Galens, K" uniqKey="Galens K">K Galens</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanehisa, M" uniqKey="Kanehisa M">M Kanehisa</name></author><author><name sortKey="Araki, M" uniqKey="Araki M">M Araki</name></author><author><name sortKey="Goto, S" uniqKey="Goto S">S Goto</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author><author><name sortKey="Madden, Tl" uniqKey="Madden T">TL Madden</name></author><author><name sortKey="Schaffer, Aa" uniqKey="Schaffer A">AA Schaffer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R Apweiler</name></author><author><name sortKey="Attwood, Tk" uniqKey="Attwood T">TK Attwood</name></author><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A Bairoch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ashburner, M" uniqKey="Ashburner M">M Ashburner</name></author><author><name sortKey="Ball, Ca" uniqKey="Ball C">CA Ball</name></author><author><name sortKey="Blake, Ja" uniqKey="Blake J">JA Blake</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="O Connor, Bd" uniqKey="O Connor B">BD O'Connor</name></author><author><name sortKey="Day, A" uniqKey="Day A">A Day</name></author><author><name sortKey="Cain, S" uniqKey="Cain S">S Cain</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stajich, Je" uniqKey="Stajich J">JE Stajich</name></author><author><name sortKey="Block, D" uniqKey="Block D">D Block</name></author><author><name sortKey="Boulez, K" uniqKey="Boulez K">K Boulez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stajich, Je" uniqKey="Stajich J">JE Stajich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Papanicolaou, A" uniqKey="Papanicolaou A">A Papanicolaou</name></author><author><name sortKey="Heckel, Dg" uniqKey="Heckel D">DG Heckel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Thain, D" uniqKey="Thain D">D Thain</name></author><author><name sortKey="Tannenbaum, T" uniqKey="Tannenbaum T">T Tannenbaum</name></author><author><name sortKey="Livny, M" uniqKey="Livny M">M Livny</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oinn, T" uniqKey="Oinn T">T Oinn</name></author><author><name sortKey="Addis, M" uniqKey="Addis M">M Addis</name></author><author><name sortKey="Ferris, J" uniqKey="Ferris J">J Ferris</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goecks, J" uniqKey="Goecks J">J Goecks</name></author><author><name sortKey="Nekrutenko, A" uniqKey="Nekrutenko A">A Nekrutenko</name></author><author><name sortKey="Taylor, J" uniqKey="Taylor J">J Taylor</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zdobnov, Em" uniqKey="Zdobnov E">EM Zdobnov</name></author><author><name sortKey="Apweiler, R" uniqKey="Apweiler R">R Apweiler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moriya, Y" uniqKey="Moriya Y">Y Moriya</name></author><author><name sortKey="Itoh, M" uniqKey="Itoh M">M Itoh</name></author><author><name sortKey="Okuda, S" uniqKey="Okuda S">S Okuda</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Conesa, A" uniqKey="Conesa A">A Conesa</name></author><author><name sortKey="Gotz, S" uniqKey="Gotz S">S Gotz</name></author><author><name sortKey="Garcia Gomez, Jm" uniqKey="Garcia Gomez J">JM Garcia-Gomez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Donlin, Mj" uniqKey="Donlin M">MJ Donlin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Conesa, A" uniqKey="Conesa A">A Conesa</name></author><author><name sortKey="Gotz, S" uniqKey="Gotz S">S Gotz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Skinner, Me" uniqKey="Skinner M">ME Skinner</name></author><author><name sortKey="Uzilov, Av" uniqKey="Uzilov A">AV Uzilov</name></author><author><name sortKey="Stein, Ld" uniqKey="Stein L">LD Stein</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Database (Oxford)</journal-id><journal-id journal-id-type="publisher-id">database</journal-id><journal-id journal-id-type="hwp">databa</journal-id><journal-title-group><journal-title>Database: The Journal of Biological Databases and Curation</journal-title></journal-title-group><issn pub-type="epub">1758-0463</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21959868</article-id><article-id pub-id-type="pmc">3263599</article-id><article-id pub-id-type="doi">10.1093/database/bar044</article-id><article-id pub-id-type="publisher-id">bar044</article-id><article-categories><subj-group subj-group-type="heading"><subject>Database Tool</subject></subj-group></article-categories><title-group><article-title>Tripal: a construction toolkit for online genome databases</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name><surname>Ficklin</surname><given-names>Stephen P.</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Sanderson</surname><given-names>Lacey-Anne</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Cheng</surname><given-names>Chun-Huai</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Staton</surname><given-names>Margaret E.</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lee</surname><given-names>Taein</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Cho</surname><given-names>Il-Hyung</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jung</surname><given-names>Sook</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bett</surname><given-names>Kirstin E.</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Main</surname><given-names>Doreen</given-names></name><xref ref-type="aff" rid="bar044-AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="bar044-COR1">*</xref></contrib></contrib-group><aff id="bar044-AFF1"><sup>1</sup>Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA, USA 99164,<sup>2</sup>Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada S7N 5B5,<sup>3</sup>Clemson University Genomics Institute (CUGI), Clemson University, Clemson, SC, USA 29634 and<sup>4</sup>Department of Computer Science, Saginaw Valley State University, University Center, MI, USA 48710</aff><author-notes><corresp id="bar044-COR1">*<bold>Corresponding author:</bold> Tel: <phone>509 335 9000</phone>; Fax: <fax>509 335 8690</fax>; Email: <email>dorrie@wsu.edu</email></corresp></author-notes><pub-date pub-type="collection"><year>2011</year></pub-date><pub-date pub-type="epub"><day>29</day><month>9</month><year>2011</year></pub-date><pub-date pub-type="pmc-release"><day>29</day><month>9</month><year>2011</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>2011</volume><elocation-id>bar044</elocation-id><history><date date-type="received"><day>1</day><month>7</month><year>2011</year></date><date date-type="rev-recd"><day>23</day><month>8</month><year>2011</year></date><date date-type="accepted"><day>29</day><month>8</month><year>2011</year></date></history><permissions><copyright-statement>© The Author(s) 2011. Published by Oxford University Press.</copyright-statement><copyright-year>2011</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.5"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at <ext-link ext-link-type="uri" xlink:href="http://tripal.sourceforge.net">http://tripal.sourceforge.net</ext-link></p></abstract><counts><page-count count="16"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Curation
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000520 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd -nk 000520 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Pmc
|étape= Curation
|type= RBID
|clé= PMC:3263599
|texte= Tripal: a construction toolkit for online genome databases
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:21959868" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |