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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
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
Tripal v3, the Collaborative Online Database Platform Supporting an International Community of Plant Genome Databases
Tripal v3, the Collaborative Online Database Platform Supporting an International Community of Plant Genome Databases
Tripal is a Drupal module
Content authoring
Security updates
Page routing
Layout
Ecosystem of modules
Highly customizable
Established community
https://www.drupal.org/about
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
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
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
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
How does Tripal do FAIR?
Metadata
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
Easy administration and curation
Metadata
Individual genes across samples
Users choose
how to group and
color samples
SchlesserSparrow
Sparrow x Schlesser
Metadata
Expression Visualization Tool
• Paste a list of genes in to get a full heatmap across all
libraries.
• Javascript allows you to zoom, download, etc.
Module Sharing:
Gene Expression Works for GDV Too
https://www.vaccinium.org/node/854703
Ontology Browser
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
Tripal v3, the Collaborative Online Database Platform Supporting an International Community of Plant Genome Databases
Cross
Site
Querying
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
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!

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Tripal v3, the Collaborative Online Database Platform Supporting an International Community of Plant Genome Databases

  • 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
  • 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
  • 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!