Talk given by Dr. Bradford Condon at the NSRP10 session of the Plant and Animal Genomes conference (PAG) 2019. Covers the basics of the biological database toolkit Tripal, and how Tripal enables FAIR data.

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

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

6. 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

7. 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

8. 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

9. 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

10. How does Tripal do FAIR?
Metadata

11. 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

12. Easy administration and curation
Metadata

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

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

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

16. Ontology Browser

17. 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

19. Cross
Site
Querying

20. 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

21. 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!