P0974 Tripal: a Construction Toolkit for Online Genome Databases

Stephen Ficklin , Washington State University, Pullman, WA
Lacey-Anne Sanderson , University of Saskatchewan, Saskatoon, SK, Canada
Chun-Huai Cheng , Washington State University, Pullman, WA
Margaret Staton , Clemson University, Clemson, SC
Sook Jung , Washington State University
Taein Lee , Washington State University
Il-Hyung Cho , Saginaw Valley State University, University Center, MI
Kirstin Bett , University of Saskatchewan, Saskatoon, SK, Canada
Dorrie Main , Washington State University
Tripal is a platform that simplifies construction of online genomic databases. With the increase in data from new sequencing technologies and downstream data analysis the need for online visualization and data-mining is ever increasing. The need for skilled web developers and IT professionals coupled with the complexities of project and data management creates an obstacle for many research communities or individual labs.  Additionally, online genomic databases are expected to provide access to the raw data, analysis results, data mining tools, cross references to larger or companion databases, include outreach content and perhaps social networking capabilities. Tripal is intended to reduce these complexities by coupling the strengths of GMOD Chado, a relational database schema for biological data, and Drupal, a popular Content Management System (CMS).  Tripal provides a web interface that includes a Chado installer, data loaders for ontologies (controlled vocabularies),  GFF files, and FASTA files.  Web pages are automatically generated for organisms, genomic features, biological libraries, and stock collections.   Web pages can be enriched with analysis results from BLAST, KAAS/KEGG, InterProScan, and Gene Ontology  (GO).  Tripal can be used “as is” but also allows for complete customization.  PHP-based template files are provided for all data types to allow for precise customizations as required by the community.  A well-developed Tripal API provides a uniform set of variables and functions for accessing any and all data within the Chado database.  Currently, Tripal only supports visualization of a subset of the current Chado schema, but further development is underway.  Meanwhile, others can use the Tripal API to develop their own extensions.  Those extensions can in turn be made available for anyone to use.  These custom extensions, the Tripal package, and access to support resources such as an active mailing list can be found on the Tripal website (http://tripal.sourceforge.net).  Currently, Tripal is in use for several genome websites including the Citrus Genome Database, The Cacao Genome Database, Pulse Crops Genomics and Breeding, The Hardwood Genomics Project and more.