Elasticsearch Indexing/Search and Expression Data Visualization with Two New Tripal Extension Modules

The Hardwood Genomics Databases (HGD) is a Tripal¹-based web database offering access to genetic and genomic data from ecologically and phylogenetically important hardwood tree species. HGD currently hosts transcriptomes from 15 species, low coverage whole genome sequence data from 10 species, SSR markers from 8 species, and the Chinese chestnut reference genome. With the rapid increase in the number of open access tree transcriptomes sequences and the accompanying gene expression data, the HWD has built new tools for researchers to search, download, and visualize this data. First, we have a new search engine, built from the open access elasticsearch² software, that provides powerful, full text search and includes features such as fuzzy searching that handle misspelled or alternately spelled words. The general site-wide search for all content types is now complemented by an advanced transcript-specific search allowing users to specify functional annotation details and filter by organism. Second, a new Tripal Expression Analysis module supports three new content types relevant to transcriptome projects: biological sample records, expression protocol records and gene expression levels for sequence features. This allows the user to explore a public RNASeq experiment fully, from collection of tissues, to lab methods and analysis of data, to gene expression levels. The feature expression levels across multiple biomaterials are visualized with interactive bar plots or heat maps that are generated with javascript graphic libraries D3JS³ and plotly⁴. Additionally, we offer a tool for users to build customized, two dimensional heat maps for gene expression comparison by submitting a list of feature IDs. The customized heat map provides detailed library information and links to the feature content pages. The implementation of these two modules in the HGD will facilitate hardwood trees research in aspects of data acquisition and discovery, exploration of candidate genes, and comparative gene expression analysis among tree species.

Keywords: Tripal, database, elasticsearch, searching, gene expression, heatmap

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

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

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

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

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