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Joint USDA-DOE Plant Genomics Knowledgebase Workshop (Jan. 8, 2010)

Workshop Report now available- click here to download report

The Plant and Animal Genome (PAG) Conference XVIII will be held January 9-13, 2010 in San Diego, California (website: http://www.intl-pag.org/). The Joint USDA-DOE Plant Genomics Knowledgebase Workshop is on January 8 from 7:30 a.m. to 6:00 p.m. This session will specifically address the requirements for effective development of data capabilities for systems biology as applied to plants, particularly relating to research and development of plant feedstocks for biofuels. The current state of plant informatics is represented by many disparate databases, primarily focusing on specific taxonomic groups or processes. To enable a systems biology approach to plant research, it is important to integrate all types of data (including molecular, morphological, and “omics” data) for bioenergy-relevant plant species. Thus, the challenge will be to develop uniformity of data format and database architectures in order to effectively integrate diverse data types and enable user-friendly acquisition and analysis.
 

Workshop Organizers
  1. Catherine Ronning, Department of Energy
  2. Susan Gregurick, Department of Energy
  3. Ed Kaleikau, U.S. Department of Agriculture
  4. Gera Jochum, U.S. Department of Agriculture
  5. Bob Cottingham, Oak Ridge National Laboratory

Charge Questions

Question 1:  What types of experimental data are currently available, and of these which format(s) are most useful/valuable? Can data from various sources and of various types be standardized into this “ideal” format to be organized and integrated into one common, searchable application

  • For example, a researcher studying cell wall biosynthesis in grasses may benefit from work being performed in poplar. How can we best facilitate cross-species comparisons? How can we use these tools to leverage knowledge gained from the model species (Arabidopsis, rice, etc.) to crop plants?

Question 2:  What are the challenges for plant bioinformatics in a 2-3 year time frame? Given the development of an integrated, uniform database (Question 1), what types of analyses do you foresee, and what types of analysis tools will maximize utility of the database?  

  • How do we best organize pathways, processes, etc., and how can we organize and distinguish common processes from taxon-specific processes? How can these informatics resources best be used to enhance plant breeding (i.e., “genotype to phenotype”)? Will these resources be effective in designing decision support tools for plant breeders in the field?

How can we best design the Knowledgebase to have the flexibility to grow with and adapt to new data and information challenges in the future?

 

List of Responses to Charge Questions
 

(Click here to read responses to the Charge Questions)

  1. Response to Charge Questions, Robin Buel
  2. Response to Charge Questions, David Douches
  3. Response to Charge Questions, Andrew Doust
  4. Response to Charge Questions, Jorge Dubcovsky
  5. Response to Charge Questions, Maria Harrison
  6. Response to Charge Questions, Thomas Lubberstedt
  7. Response to Charge Questions, Seth C. Murray
  8. Response to Charge Questions, David Neale
  9. Response to Charge Questions, Zhaohua Peng
  10. Response to Charge Questions, Steve Strauss
  11. Response to Charge Questions, Janice Zale
  12. Response to Charge Questions, Peijian Cao, Manfred Zorn, and Pamela Ronald
  13. Response to Charge Questions, Jeffrey Ross-Ibarra
  14. Response to Charge Questions, Dong Wang
  15. Response to Charge Questions, E. Beers, A. Dickerman, and A. Brunner
  16. Response to Charge Questions, Patrick Byrne
  17. Response to Charge Questions, Tim Close
  18. Response to Charge Questions, Sam Hazen
  19. Response to Charge Questions, Eva Huala
  20. Response to Charge Questions, Scott Jackson
  21. Response to Charge Questions, Christian Tobias
  22. Response to Charge Questions, Wilfred Vermerris
  23. Response to Charge Questions, John Vogel
  24. Response to Charge Questions, David Francis
  25. Response to Charge Questions, Matias Kirst
  26. Response to Charge Questions, Katrien M. Devos
  27. Response to Charge Questions, Pam Green
  28. Response to Charge Questions, Ismail Dweikat
  29. Response to Charge Questions, Jan Leach
  30. Response to Charge Questions, Luca Comai
  31. Response to Charge Questions, Charles Brummer
  32. Response to Charge Questions, Jerry Tuskan
  33. Response to Charge Questions, Richard Veilleux
  34. Response to Charge Questions, Steve Rounsley
  35. Response to Charge Questions, Phil McClean
  36. Response to Charge Questions, T. M. Davis
  37. Response to Charge Questions, Victor Busov
  38. Response to Charge Questions, Andy Pereira
  39. Response to Charge Questions, Lukas Mueller

  40. Response to Charge Questions, Jim Giovannoni

Agenda and Location of Meeting Room

Click here to view the Agenda. The Workshop will be held in the Pacific Salon 3 room. 

 

List of Abstracts

(Click here to read Abstracts)
  
  1. Brachypodium distachyon: A New Model for the Grasses, John Vogel
  2. Development of Genomic and Genetic Tools for Foxtail Millet: Use of These Tools in the Improvement of Biomass Production for Bioenergy Crops, J. L. Bennetzen and K. M. Devos
  3. GRIN-Global: An International Project to Develop a Global Plant Genebank Information Management System, P. Bretting, G. Kinard, P. Cyr, B. Weaver, M. Millard, C. Gardner, M. Bohning, G. Emberland, Q. Sinnott, J. Postman, K. Hummer, T. Ayala-Silva, T. Franco, M. Mackay, and L. Guarino
  4. Advancing the Barley Genome, Timothy J. Close, Stefano Lonardi, Jeffrey L. Bennetzen, and Gary J. Muehlbauer
  5. Genome Sequence for the Common Bean, Scott Jackson, Phil McClean, Jeremy Schmutz, and Dan Rokhsar
  6. BeanCAP – A NIFA Coordinated Agricultural Project, Phillip E. McClean
  7. Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics and Breeding for Gene Discovery and Barley Improvement, Gary J. Muehlbauer
  8. Bioinformatics Use in Advancing Plant Genomics, Genetics and Breeding: The Plant Breeders Perspective, David Francis

List of Presentations

 

9. Introduction to the Plant Knowledgebase Workshop, Catherine Ronning 10. DOE Systems Biology Knowledgebase, Bob Cottingham 11. A Plant Breeding Perspective, David Francis 12. The iPlant Collaborative, Steve Rounsley 13. Leveraging Arabidopsis Data for Research on Other Plant Species, Eva Huala 14. US-EC Plant Bioinformatics, Doreen Ware 15. Genomes as an "Organizing Principle" for the Knowledgebase, Dan Rokhsar 16. Plant Knowledgebase Breakout Group 1 Summary 17. Plant Knowledgebase Breakout Group 2 Summary 18. Plant Knowledgebase Breakout Group 3 Summary 19. Plant Knowledgebase Breakout Group 4 Summary

Kbase Workshop Summary Report

 Posted March 19, 2010

Subpages (4): Abstracts Charge Questions Map of Convention Center Presentations
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