Abstract

Tripal is an open-source freely available toolkit for construction of online genomic and genetic databases. It aims to facilitate development of community-driven biological websites by integrating the GMOD Chado database schema with Drupal, a popular website creation and content management software. Tripal provides a suite of tools for interaction with a Chado database and display of content therein. The tools are designed to be generic to support the various ways in which data may be stored in Chado. Previous releases of Tripal have supported organisms, genomic libraries, biological stocks, stock collections and genomic features, their alignments and annotations. Also, Tripal and its extension modules provided loaders for commonly used file formats such as FASTA, GFF, OBO, GAF, BLAST XML, KEGG heir files and InterProScan XML. Default generic templates were provided for common views of biological data, which could be customized using an open Application Programming Interface to change the way data are displayed. Here, we report additional tools and functionality that are part of release v1.1 of Tripal. These include (i) a new bulk loader that allows a site curator to import data stored in a custom tab delimited format; (ii) full support of every Chado table for Drupal Views (a powerful tool allowing site developers to construct novel displays and search pages); (iii) new modules including ‘Feature Map’, ‘Genetic’, ‘Publication’, ‘Project’, ‘Contact’ and the ‘Natural Diversity’ modules. Tutorials, mailing lists, download and set-up instructions, extension modules and other documentation can be found at the Tripal website located at http://tripal.info.Database URL: http://tripal.info/

Highlights

  • The human genome project, one of the largest genome sequencing projects undertaken, began in 1990 at an initial cost estimate of $3 billion

  • The project took 13 years to complete by a large international group of collaborators and produced a high-quality genome assembly [1]

  • A list of simple search tools is provided to the user under a menu item called ‘Search Biological Data’. Because these simple search tools are created using Drupal Views, the site developer can later customize these default Views, or create new ones for more advanced functionality or to handle different data types not yet integrated into the default Tripal templates

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Summary

Introduction

The human genome project, one of the largest genome sequencing projects undertaken, began in 1990 at an initial cost estimate of $3 billion. Tripal release v1.0 (March 2013) supported the Chado version 1.2, added improvements in performance for the GFF, FASTA and OBO loaders, used database transactions for data loading, added new modules supporting Maps (genetic and genomic) and the new natural diversity tables of Chado v1.2 [9]. Tripal provides a web interface for allowing the addition of custom tables by a site developer.

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