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

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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.

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

  1. 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. 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. 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. 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. 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. 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. 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. 8. How does Tripal do FAIR? Metadata
  9. 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. 10. Easy administration and curation Metadata
  11. 11. Individual genes across samples Users choose how to group and color samples SchlesserSparrow Sparrow x Schlesser Metadata
  12. 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. 13. Module Sharing: Gene Expression Works for GDV Too https://www.vaccinium.org/node/854703
  14. 14. Ontology Browser
  15. 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. 16. Cross Site Querying
  17. 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. 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!

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