P0473
Enhancement of Data Searching, Visualization and Exploration in the Hardwood Genomics Database (HGD) by Integration of New Tripal Extensions and Galaxy

Ming Chen , University of Tennessee, Knoxville, TN
Nate Henry , University of Tennessee, Knoxville, TN
Thomas Lane , University of Tennessee, Knoxville, TN
Xiao Zhou , University of Tennessee, Knoxville, TN
Anthony Bretaudeau , INRIA/Irisa - Campus de Beaulieu, RENNES, France
Jill L. Wegrzyn , Department of Ecology and Evolutionary Biology - University of Connecticut, Storrs, CT
Stephen P. Ficklin , Washington State University, Pullman, WA
Margaret Staton , University of Tennessee, Knoxville, TN
The Hardwood Genomics Databases (HGD) is a Drupal1/Tripal2-based web database which uses Chado3 schema to store genetic and genomic data from ecologically and phylogenetically important hardwood tree species. One important goal of the HGD research group is to develop Tripal extension modules and/or integrate other tools to enhance the accessibility, visualization and exploration of genetic resources that are housed in the HGD. The HGD research group has developed two new Tripal extension modules: the Tripal Elasticsearch module and the Tripal Expression Analysis module. The Tripal Elasticsearch module uses the powerful elasticsearch4 as its search engine, providing parallel, scalable indexing and general search of the entire Tripal site as well as constrained search of targeted Chado database tables and table fields. The module allows customization of search form interfaces and formatting of search results. Search form interfaces and search results for each indexed data units are displayed in individual Drupal blocks, which provides high flexibility of rendering search results. The Tripal Expression Analysis module creates four content types to store and display information about biological materials, analysis protocols, array designs and gene expression levels of sequence features. Patterns of gene expression across RNASeq libraries are visualized with heat maps or bar plots created with javascript graphic libraries D3JS5 or plotly6. A one-dimensional heat map or bar chart is provided for each feature page to visualize the gene expression level across all available biomaterials. Two-dimensional, customized heat maps can be built from user specified list of genes via a search form interface for gene expression comparison. The HGD group is also collaborating with other Tripal databases groups on integrating a Galaxy7 analysis server with Tripal databases. A set of galaxy workflows have been developed and will be wrapped into a Tripal galaxy gateway that is being developed by our collaborative groups. The Tripal database will run galaxy server as a data analysis backend and provide users with efficient approaches for exploring and analyzing data housed in the database.

Keywords: Tripal, database, elasticsearch, gene expression, galaxy, workflows

1. Drupal - Open Source CMS. https://www.drupal.org/ Accessed Oct 24, 2016.

2. Ficklin, Stephen P., et al. "Tripal: a construction toolkit for online genome databases." Database 2011 (2011): bar044.

3. Mungall, Christopher J., and David B. Emmert. "A Chado case study: an ontology-based modular schema for representing genome-associated biological information." Bioinformatics 23.13 (2007): i337-i346.

4. Elasticsearch. https://www.elastic.co/. Accessed Oct 24, 2016.

5. D3JS. https://d3js.org/. Accessed Oct 24, 2016

6. Plotly. https://plot.ly/. Accessed Oct 24, 2016

7. Goecks, Jeremy, Anton Nekrutenko, and James Taylor. "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences." Genome biology 11.8 (2010): 1.


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