Tripal: a construction toolkit for online genome databases

Overview
TitleTripal: a construction toolkit for online genome databases
AuthorsFicklin SP, Sanderson LA, Cheng CH, Staton ME, Lee T, Cho IH, Jung S, Bett KE, Main D
TypeJournal Article
Journal NameDatabase : the journal of biological databases and curation
Volume2011
IssueN/A
Year2011
Page(s)bar044
CitationFicklin SP, Sanderson LA, Cheng CH, Staton ME, Lee T, Cho IH, Jung S, Bett KE, Main D. Tripal: a construction toolkit for online genome databases. Database : the journal of biological databases and curation. 2011; 2011:bar044.

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 http://tripal.sourceforge.net.

Author Details
Additional information about authors:
Details
1Stephen P Ficklin
Affiliation : Washington State University. Pullman, WA. USA
2Lacey-Anne Sanderson
3Chun-Huai Cheng
4Margaret E Staton
5Taein Lee
6Il-Hyung Cho
7Sook Jung
Affiliation : Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA. sook@genome.clemson.edu
8Kirstin E Bett
9Doreen Main
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:21959868
Properties
Additional details for this publication include:
Property NameValue
Publication ModelElectronic-Print
ISSN1758-0463
eISSN1758-0463
Publication Date2011
Journal AbbreviationDatabase (Oxford)
DOI10.1093/database/bar044
Elocation10.1093/database/bar044
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Journal CountryEngland
Publication TypeResearch Support, Non-U.S. Gov't
Publication TypeResearch Support, U.S. Gov't, Non-P.H.S.