Efforts by the Hardwood Genomics Database team to extend Tripal functionality

The Hardwood Genomics Database team at the University of Tennessee is working to extend the functionality of Tripal by (1) providing a method to easily load and display variable gene expression data in Chado and (2) providing intuitive search tools utilizing the Elasticsearch search engine. Both solutions will be implemented as modules that can be installed in current Tripal websites.

The gene expression module is being developed in an effort to create a standard way to store and display variable expression data in chado, including experimental data derived from RNAseq. In order to be compatible with current Chado databases, tables from the Chado MAGE module were chosen as a method for storing expression data. Tripal data loaders will be provided for the most common expression output formats, and the expression data across different samples (tissues, treatments or other) will be displayed on the feature page.

The Tripal Elasticsearch module is intended to be a replacement for the standard Drupal search functionality as well as an improvement on the search functionality provided by Drupal Views. After implementing the Elasticsearch server software, the Tripal Elasticsearch module will enable the indexing of Drupal nodes as well as all records in the Chado database. The search interface for users will allow a broad site-wide search as well as searches customizable by organism, data type or other limits.

Both the Tripal gene expression module and the Tripal Elasticsearch module will be made publicly available along with a manual to guide implementation.