Tripal: A construction toolkit for online genome databases

Stephen P Ficklin; Lacey-Anne Sanderson; Chun-Huai Cheng; Margaret E Staton; Taein Lee; Il-Hyung Cho; Sook Jung; Kirstin E Bett; Doreen Main

doi:10.1093/database/bar044

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Tripal: A construction toolkit for online genome databases

Journal article

Open access

Peer reviewed

Tripal: A construction toolkit for online genome databases

Stephen P Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret E Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E Bett and Doreen Main

Database : the journal of biological databases and curation, Vol.2011, pp.bar044-bar044

2011

DOI: https://doi.org/10.1093/database/bar044

Handle:

https://hdl.handle.net/2376/115644

PMCID: PMC3263599

PMID: 21959868

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Abstract

Databases, Genetic

Internet

Genome

Database Management Systems

Data Mining

Computational Biology

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.

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Title: Tripal: A construction toolkit for online genome databases
Creators: Stephen P Ficklin - Department of Horticulture and Landscape Architecture, Washington State University, Pullman, WA 99164, USA
Lacey-Anne Sanderson
Chun-Huai Cheng
Margaret E Staton
Taein Lee
Il-Hyung Cho
Sook Jung
Kirstin E Bett
Doreen Main
Publication Details: Database : the journal of biological databases and curation, Vol.2011, pp.bar044-bar044
Academic Unit: Horticulture, Department of
Publisher: England
Identifiers: 99900547970501842
Language: English
Resource Type: Journal article