Contribution of standards for developing networks, crop ontologies and a global portal to provide access to plant genetic resources


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Presentation by Adriana Raquel Alercia (Bioversity International) at the IAALD 2010 World Congress - 26-29 April 2010, Montpellier, France

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  • Contribution of standards for developing networks, crop ontologies and a global portal to provide access to plant genetic resources

    1. 1. IAALD - XIII World Congress Contribution of standards to developing networks, crops ontology and global portals to provide access to plant genetic resources Adriana Alercia, Michael Mackay Bioversity International, HQ Montpellier, 29 April 2010
    2. 2. Crop Standards <ul><ul><li>USDA-GRIN </li></ul></ul><ul><ul><li>UPOV </li></ul></ul><ul><ul><li>COMECON </li></ul></ul><ul><ul><li>BIOVERSITY (ex-IPGRI) </li></ul></ul>
    3. 3. BIOVERSITY DESCRIPTORS AND DERIVED STANDARDS <ul><li>Crop descriptors </li></ul><ul><li>FAO/IPGRI </li></ul><ul><li>Multicrop Passport </li></ul><ul><li>Descriptors </li></ul><ul><li>Descriptors for </li></ul><ul><li>Genetic Marker </li></ul><ul><li>Technologies </li></ul><ul><li>Descriptors for Farmers Knowledge of Plants </li></ul>
    4. 4. Brief History of Bioversity Standards <ul><li>Minimum lists for crops (1977) </li></ul><ul><li>Comprehensive lists for crops (1988) </li></ul><ul><li>Highly discriminating descriptors for crops (1993) </li></ul><ul><li>FAO/IPGRI Multicrop passport descriptors (1997 - 2001) </li></ul><ul><li>Descriptors for Genetic Marker Technologies (2004) </li></ul><ul><li>Descriptors for Farmers Knowledge about plants (2009) </li></ul>
    5. 5. Development Process <ul><ul><li>Drafting of crop descriptors led by an expert(s) </li></ul></ul><ul><ul><li>Draft version prepared with Bioversity </li></ul></ul><ul><ul><li> international accepted format </li></ul></ul><ul><ul><li>Broad group of scientists is invited to provide </li></ul></ul><ul><ul><li> comments </li></ul></ul><ul><ul><li>Bioversity’s scientists are consulted for technical </li></ul></ul><ul><ul><li> /scientific comments </li></ul></ul><ul><ul><li>Relevant comments are included in the draft </li></ul></ul><ul><ul><li>Author(s) receives the text for final approval </li></ul></ul><ul><ul><li>List is prepared for publication </li></ul></ul>
    6. 6. Crop Standards Passport Management Environment and site Characterization Evaluation
    7. 7. FAO/IPGRI (MCPD) Passport Standard <ul><li>List of common passport </li></ul><ul><li>descriptors </li></ul><ul><li>Fields identifying the accession </li></ul><ul><li>are mandatory </li></ul><ul><li>Combination of mandatory </li></ul><ul><li>fields has to be unique </li></ul><ul><li>Preferred language: English </li></ul><ul><li>Multiple values separated by a </li></ul><ul><li>semicolon (;) </li></ul><ul><li>Dates recorded as </li></ul><ul><li>YYYYMMDD </li></ul>
    9. 9. Descriptors for Genetic Marker Technologies  Descriptors targeted to researchers using genetic marker technologies to generate and exchange genetic marker data that are standardized and replicable  Minimum set of descriptors needed to describe a marker technology used with a particular plant species
    10. 10. Standards for Farmers’ Knowledge <ul><li>This is a first attempt to create a lingua franca to capture and share information amongst farmers and scientists and to integrate biology and traditional knowledge. </li></ul><ul><li>This tool aims to document the holdings of a community as groups of items, which complement the more traditional crop-level descriptors such as those that are produced for a single crop. </li></ul><ul><li>Bioversity descriptors are a knowledge base that makes TK of people and plants more useful to farmers, researchers and conservers </li></ul>
    11. 11. Traditional Knowledge: Link between Standards and Farmers’ Knowledge sharing INTO DATABASES AND PORTALS FARMERS’ KNOWLEDGE SCIENTISTS’ KNOWLEDGE STANDARDIZED DOCUMENTATION WITH DESCRIPTOR LISTS TO SCIENTIFIC COMMUNITY TO FARMING COMMUNITY? A Generic Database for Integrating Genotypic and Phenotypic Information for PGR
    12. 12. Some expected benefits from Farmers Standard <ul><li>Increased uniformity of documentation </li></ul><ul><li>Increased visibility of farmers’ work </li></ul><ul><li>Increased scientific validity of farmers’ knowledge </li></ul><ul><li>Increased ability to work across geographic and knowledge boundaries </li></ul><ul><li>Contribute to development of databases </li></ul><ul><li>Facilitate data exchange </li></ul><ul><li>Create a platform to share farmers knowledge </li></ul>
    13. 13. Contribution of Standards: Global portals and Crop networks MCPD GCP ontologies                                                         
    14. 14. Contributing to Networks: SINGER, A network of Genebanks Landraces Wild species Advanced cultivars 27 % 59 % 14 % <ul><li>11 CGIAR genebanks </li></ul><ul><li>>600,000 accessions </li></ul><ul><li>>11% world holdings </li></ul><ul><li>well documented </li></ul><ul><li>mostly landraces </li></ul><ul><li>A Global Public Good </li></ul>
    15. 15. How information is shared? Passport Characterization Evaluation Multi-crop Descriptors MCPD
    16. 16. Contributing to Networks: EURISCO: A network of Genebanks <ul><li> It is an European Search Catalogue with passport information on ex situ collections, accessible via Internet - More than 1.1 million accessions, 31 National Inventories from 35 countries </li></ul><ul><li> Passport data based on MCPD Standard </li></ul>
    17. 17. How information is shared? <ul><ul><li>possibility of automation </li></ul></ul><ul><ul><li>can be kept up-to-date </li></ul></ul><ul><ul><li>result: monitor </li></ul></ul><ul><li>ONE CENTRAL CATALOGUE </li></ul><ul><li>fixed set of data suppliers </li></ul><ul><li>one transaction per genebank </li></ul>MCPD nat. inven-tory nat. inven-tory nat. inven-tory nat. inven-tory nat. inven-tory nat. inven-tory nat. inven-tory nat. inven-tory gene- bank gene- bank gene- bank gene- bank gene- bank gene- bank gene- bank gene- bank gene- bank gene- bank gene- bank gene- bank
    18. 18. Contributing to DBs: The Musa Germplasm information System (MGIS)
    19. 19. Contributing to DBs: Coconut Genetic Resources Database CGRD Courtesy of Chantal Hamelin,CIRAD
    20. 20. Coverage of Descriptors <ul><ul><li>Bioversity Standards for 100 crops represent 3.5 millions accessions held in genebanks worldwide, and </li></ul></ul><ul><ul><ul><li>90% - International Treaty – Annex 1 </li></ul></ul></ul><ul><ul><ul><li>95% - CGIAR centres mandate crops </li></ul></ul></ul><ul><ul><li>Additionally, 34% of Crop Descriptors deal with Neglected and Underutilized crops </li></ul></ul>
    21. 21. <ul><ul><li>1996 – ITCPGR, Germany – 102 CR - 91% (EPMR) </li></ul></ul><ul><ul><li>1999 – CG Secretariat – 146 Curators – banana, coconut and maize - 69% </li></ul></ul><ul><ul><li>2007 – CCER external review – Impact Study - 86% </li></ul></ul>Impact Assessments on Bioversity Descriptors
    22. 22. Importance of different types of descriptors (CCER, 2007) Essential or Somewhat Not used at all important important BIOVERSITY 86% 10% 4% UPOV 52% 18% 30% USDA-GRIN 33% 22% 44% COMECON 8% 15% 77%
    23. 23. Types of organizations using descriptors and derived standards (CCER, 2007)
    24. 24. Some benefits (CCER, 2007) <ul><li>Contributed to development of databases </li></ul><ul><li>Increased uniformity of documentation </li></ul><ul><li>Increased ability to work with other partners </li></ul><ul><li>Facilitated data exchange </li></ul><ul><li>Enabled greater efficiency in collections identifying and reducing duplication </li></ul><ul><li>Helped to develop core collections </li></ul><ul><li>Increased use of accessions by helping potential users to select germplasm </li></ul>
    25. 25. CONCLUSIONS <ul><li>Bioversity descriptors are a knowledge base that makes collections of crop diversity more useful to researchers, plant breeders, farmers and conservers </li></ul><ul><li>The participatory process worldwide has helped to validate and support widespread use of Bioversity Descriptors </li></ul><ul><li>Bioversity descriptors have an impact at the global level and major benefits are substantial </li></ul>
    26. 26. THANK YOU!