New extension software modules to enhance searching and display of transcriptome data in Tripal databases

Abstract

Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data. It consists of a set of core modules that deliver essential functions for loading and displaying data records and associated attributes including organisms, sequence features and genetic markers. Beyond the core modules, community members are encouraged to contribute extension modules to build on the Tripal core and to customize Tripal for individual community needs. To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules. Tripal Elasticsearch enables fast, scalable searching of the entire content of a Tripal site as well as the construction of customized advanced searches of specific data types. We demonstrate the use of this module for searching assembled transcripts by functional annotation. A second module, Tripal Analysis Expression, houses and displays records from gene expression assays such as RNA sequencing. This includes biological source materials (biomaterials), gene expression values and protocols used to generate the data. In the case of an RNASeq experiment, this would reflect the individual organisms and tissues used to produce sequencing libraries, the normalized gene expression values derived from the RNASeq data analysis and a description of the software or code used to generate the expression values. The module will load data from common flat file formats including standard NCBI Biosample XML. Data loading, display options and other configurations can be controlled by authorized users in the Drupal administrative backend. Both modules are open source, include usage documentation, and can be found in the Tripal organization’s GitHub repository. Database URL: Tripal Elasticsearch module: https://github.com/tripal/tripal_elasticsearch Tripal Analysis Expression module: https://github.com/tripal/tripal_analysis_expression

Growing and cultivating the forest genomics database, TreeGenes

“…This feature permits each Tripal database to define their terms, and therefore provides a mechanism to search the same data types across Tripal databases, regardless of how they are stored. An extension on this framework developed by Hardwood Genomics Web includes Tripal ElasticSearch ( 7 ). This module allows Tripal sites to index the content they would like to share and provides an interface for cross-site query.…”

15 years of GDR: New data and functionality in the Genome Database for Rosaceae

“…During the last 5 years, we also made advances in curating data with more ontologies and incorporating ontologies in data query pages to facilitate data-sharing across different data types, species and databases. Future effort will include further developing MapViewer to integrate genome data and genetic maps, providing an enhanced querying interface, expanding analysis capabilities in BIMS through access to additional functionality, integrating Galaxy analysis platform through Tripal Galaxy module (https://www.drupal.org/project/tripal_galaxy), providing access to High Performance Computing and enabling cross-Tripal databases querying capability using Tripal Elasticsearch (56) and Tripal Exchange (http://tripal.info/tutorials/v3.x/web-services).…”

Tripal Developer Toolkit

“…If the rename method is updated with new code, tests are rerun to ensure no new bugs have been in inadvertently created by the new additions. Tests are so helpful that some development practices prescribe writing tests before writing the intended code (Test Driven Development), which can increase test coverage and coding efficiency (10). Despite their importance, a novice Tripal developer may be intimidated by the overhead required for writing reproducible, platform independent tests that interact with Chado, Drupal, and Tripal.…”

“…Extension modules can then be developed by any group to extend the core and provide additional functionality. Examples of extension modules include a BLAST tool for users (7) , natural diversity genotype data loader and display (8) (9) , and elasticsearch to provide fast sitewide searching (10) . Tripal websites cost less to build and maintain, and they can reuse and share Tripal extension modules, meaning each website is not coding its own solution to shared biological problems.…”