1.
Tripal v3, the Collaborative Online Database Platform
Supporting an International Community of Plant Genome
Databases
Bradford Condon, Stephen Ficklin, Meg Staton
Hardwood Genomics/University of Tennessee Knoxville, i5k NAL/USDA
@bradfordcondon

2.
A web framework for genetic and genomic data
Goals:
• Simplify construction of websites that have biological
data
• Encourage high-quality, standards-based websites
for data sharing and collaboration
• Reuse code across databases
http://tripal.info
https://tripal.readthedocs.io/en/latest/user_guide.html

3.
Tripal is a Drupal module
Content authoring
Security updates
Page routing
Layout
Ecosystem of modules
Highly customizable
Established community
https://www.drupal.org/about

4.
Tripal Core Functions
● Load, Store, and Display
Chado Content
○ Organisms
○ Contacts
○ Analyses
○ Features
● Map Controlled Vocabularies
● Jobs Management
● Web Services
https://github.com/GMOD/Chado

5.
Example Extension Modules
• Transcriptomes
• Functional annotation:
• BLAST
• KEGG
• InterPro
• Gene Ontology
• BLAST server
• Breeding API
• NCBI data Import
https://tripal.readthedocs.io/en/latest/extensions.html
• Genetic and Physical
Maps
• Jbrowse
• Apollo
• Galaxy
• Stocks/Germplasm
• Phenotypes
• Genotypes
• Phylogenies
• Gene expression data

6.
Cooperative Database
Development
• Washington State University
• University of Saskatchewan
• University of Tennessee,
Knoxville
• Iowa State University
• University of Connecticut
• USDA National Agricultural
Library
• Bioversity International (France)
13 code
contributors
64 modules on
GitHub
electively
tagged as tripal
https://github.com/topics/tripal

7.
Tripal s FAIR
Why do we care?
• FAIR emphasizes
helping machines to
find and reuse data
• Make your life easier
(biologist)
• Write new tools and
code that will work
with all data

8.
How does Tripal do FAIR?
Metadata

9.
Expression Module
Biological
Samples
RNA Libraries Gene Expression
Levels
Need a better way to store and visualize RNASeq differential gene
expression experiments.
https://github.com/tripal/tripal_analysis_expression

10.
Easy administration and curation
Metadata

11.
Individual genes across samples
Users choose
how to group and
color samples
SchlesserSparrow
Sparrow x Schlesser
Metadata

12.
Expression Visualization Tool
• Paste a list of genes in to get a full heatmap across all
libraries.
• Javascript allows you to zoom, download, etc.

13.
Module Sharing:
Gene Expression Works for GDV Too
https://www.vaccinium.org/node/854703

14.
Ontology Browser

15.
Elasticsearch Software
Open source search engine
• Features - autocomplete, fuzzy searching, “did you mean”
suggestions
Tripal Elasticsearch
• Full administrative control of content indexing
• Can search all content
• Much easier for software developers to use
• Easily build advanced search forms
• Preconfigured indices for Chado data
Findable

16.
Cross
Site
Querying

17.
Conclusions
• Tripal 3 can make FAIR possible for
your data
• Tripal already has lots of modules to
support common data types
• Organism, feature, expression, search
• Tools - GMOD
• Tripal allows small communities to
“have their cake and eat it too”
• Sharing and reusing code
• Interoperability at database and site level
with other databases
• Customizable user experience

18.
Abdullah Almsaeed
Research Associate
Stephen Ficklin
Dorrie Main
Jill Wegrzyn
Bert Abbott
Dana Nelson
Meg Staton
Abdullah Almsaeed
Chris Childers
Monica Poelchau
https://www.hardwoodgenomics.org/
http://tripal.info/
Tripal Session this afternoon!