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An international project to develop a global plant genebank information management system

An international project to develop a global plant genebank information management system.

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An international project to develop a global plant genebank information management system

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  1. An international project to develop a global plant genebank information management system P. Bretting, G. Kinard, P. Cyr, B. Weaver, M. Millard, C. Gardner, R. Little, M. Bohning, G. Emberland, L. Gu, M. Reisinger, Q. Sinnott, J. Postman, K. Hummer, T. Ayala-silva, T. franco, M. Mackay, and L. guarino

  2. Are plant genebanks simply giant freezers? No!

  3. Plant Genetic Resource Management in Genebanks • Acquisition • Maintenance • Regeneration • Documentation and Information Management • Distribution • Characterization • Evaluation • Enhancement • Research to increase curatorial efficiency and effectiveness

  4. USDA National Plant Germplasm System (NPGS)

  5. One of the largest national genebank systems. More than 530,000 samples of more than 13,300 plant species. Large collections of the major staple crops important to U. S. and world agriculture. Large holdings of crops without major collections at international agricultural research centers, e.g., cotton, soybean, various horticultural and “specialty” crops. Germplasm Resources Information Network (GRIN): a national standard. The USDA National Plant Germplasm System (NPGS)

  6. GRIN • GRIN = Germplasm Resources Information Network. http://www.ars-grin.gov/ The genebank information management system for the NPGS, and for Canada’s genebank system (GRIN-Canada). • The Global Crop Diversity Trust asked ARS and Bioversity International (an International Agricultural Research Center) to enhance and expand GRIN to address global germplasm information management needs. • In 2008, the Trust awarded ARS a 3-year, $1.4 million grant to develop GRIN-Global; ARS is devoting more than $1 million of in-kind support to the project.

  7. GRIN-Global • Based on GRIN, but can be implemented in either network systems or in a “stand-alone” local management mode. • Supports users via a “user-friendly” interface. • Supports linkages with other databases and interoperability with existing systems. • Advanced querying, custom and third-party applications, on-line ordering/request capabilities. • Designed to be the global standard plant genebank information management system.

  8. Three Tier Architecture

  9. Three Tier Architecture • Web Service-based • Shares structured data between all clients and the business tier via XML. • Adaptable and flexible • Readily adaptable to changes in operating systems (client can be ported to many platforms). • Easier to make changes to individual tiers without affecting the other tiers. • Example: MaizeGDB – proof of concept for the openness of web services. • Provides on-demand maize accession inventory availability from GRIN real-time at the MaizeGDB website. • Web service uses .NET 3.5. • Client PHP application at MaizeGDB consumes data from the .NET web service.

  10. Two Primary Applications • Desktop Client (on local machine) • Curator’s tool • Distributed to, and implemented by, genebanks. • Designed for genebank data inserts/updates/deletes. • Feature-rich application support curator’s tasks. • Targeted to operating systems that implement the .NET 3.5 framework. • Browser/thin client or rich (thick) client (such as a non-Windows application or PDA, smart phone, etc.) • Open public interface • Designed for information searches and germplasm ordering by researchers, breeders, and educators.

  11. Features particularly relevant to geneticists, genome researchers and breeders • Mechanisms for readily uploading and downloading accession evaluation (e.g. trait) and characterization (e.g. genetic marker) data in a spreadsheet format. • Interoperability between GRIN-Global and genome databases will enable researchers to order genebank accessions based on genomic data, and also enable curators to keep track of plant genetic resource use in such research.

  12. Features particularly relevant to curators, geneticists, breeders, and genome researchers • Ability to readily update and refine descriptors and descriptor definitions, and link data to original research papers or evaluation/characterization projects. • Powerful, yet easy-to-use data query/mining tools (e.g., customizable reporting and viewing formats) for comparing multiple trait features and genetic marker profiles; identifying unique genetic variants; and culling genetically redundant materials etc.

  13. Timelines and Products

  14. Accessible to all--free and without restriction • All source code (including the database schema) is in the public domain and will be freely distributed. • All system components can be modified/enhanced using software development tools that are free. • Microsoft .NET Framework 3.5 • SVN version control system • Visual Studio Express 2008 • Written to support free database systems. • MySQL Community database • PostgreSQL • Oracle Express • Microsoft SQL Server Express

  15. International collaboration makes it possible • Global Crop Diversity Trust– Cary Fowler, Luigi Guarino • USDA/ARS– Peter Bretting, Peter Cyr, Mark Millard, Candice Gardner, Lisa Burke, Gary Kinard, Gorm Emberland, Quinn Sinnott, Martin Reisinger, Laura Gu, Joseph Postman, Kim Hummer, Tomás Ayala-Silva, Harold Bockelman. • Bioversity – Michael Mackay (Italy), Tito Franco (Colombia), Fawzy Nawar (Italy), Fred Atieno (Kenya), Brock Weaver (USA), Rachelle Little (USA) • EMBRAPA (Brazil)-- Patricia Goulart Bustamante • Crop Research Institute (Czech Republic) – Iva Faberová • INTA (Argentina) – Julio Tilleria • Technical Steering Group– Bill Gelbart (Harvard), David Austin (Pioneer/DuPont), Bill Tracy (Univ. Wisconsin), Fred Bliss (Seminis), Harold Bockelman (USDA/ARS), Michael Mackay (Bioversity), Tito Franco (Bioversity), Julio Tilleria (INTA-Argentina)

  16. We Need Your Input! http://www.grin-global.org/ • We need your help and input to develop the use cases and work flows for GRIN-Global. • Please participate in the GRIN-Global open forum at this address: http://www.grin-global.org/forums/

  17. GRIN-Global Demonstration and Poster at PAG • Demonstration: Monday 11 January 2009, 2:10 -2:30 PM, in California Room: “The GRIN-Global Information Management System: A Preview and Opportunity for Public User Input” by Pete Cyr et al. • Poster CP922: Monday 11 January 2009, 10:00-11:30 AM, in Exhibit Hall. http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_922.html

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