New Tripal Extensions: Elasticsearch and Gene Expression Visualization

Tripal extension modules have become an essential part of the Tripal software ecosystem by providing flexible and customizable interfaces for new datatypes while leveraging the functionality and stability of the core modules 1 . In order to build new search capabilities and data visualizations for transcriptome data in the Hardwood Genomics Database HGD, www.hardwoodgenomics.org ), we have developed two new extension modules. Tripal Elasticsearch leverages the widely adopted, open source ElasticSearch engine to deploy fast, scalable searching of a Tripal website encompassing data from both the Drupal database and the Chado database 2 . The module provides a default site-wide search option as well as advanced searches of specific tables by individual fields. The administrative backend controls indexing for each individual Chado table, customization of search forms, and formatting of search results. The second module, Tripal Expression Analysis, stores and displays two data types: RNA biomaterial library records and normalized gene expression values derived from RNA sequencing of those biomaterials. A heatmap of gene expression across all available biomaterials is built and displayed for each gene page. Additionally, the module provides a web form interface to build custom heat maps from a user-specified list of genes. The heat maps are built with the javascript graphics libraries d3 and plotly to provide user interaction with the image, including zoom, pan, hover, and click. The beta version of both modules are available in the Tripal GitHub repository and may be viewed in use at the HGD. Key Words: database, Chado, Tripal, searching, transcriptome, gene expression, heatmap 1 Ficklin SP, Sanderson L-A, Cheng C-H, et al (2011) Tripal: a construction toolkit for online genome databases. Database 2011:bar044. 2 Mungall CJ, Emmert DB, others (2007) A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics 23:i337–i346.