Major germplasm data sources and referatories

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Presentation of some of the major germplasm data sources, including aggregators, networks and individual data providers. Information based on the agINFRA Dossier on Germplasm Data sources (available at http://wiki.aginfra.eu/index.php/Germplasm_Working_Group)

Presented during Session 3 of the 1st International e-Conference on Germplasm Data Interoperability (https://sites.google.com/site/germplasminteroperability/)

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Major germplasm data sources and referatories

  1. 1. Major germplasm data sources and referatories Dr. Vassilis Protonotarios Agro-Know Technologies, Greece Dr. Guntram Geser Salzburg Research, Austria e-Conference on Germplasm Data Interoperability Session 3: “Setting up an infra for the Germplasm Data”
  2. 2. Structure of the presentation 1. 2. 3. 4. Introduction Germplasm data aggregators Germplasm data sources Conclusions
  3. 3. Aim of presentation • To provide an overview of the major germplasm data sources – Not possible to cover all of them – Information mostly based on “agINFRA Dossier on Germplasm Information” (2012)
  4. 4. Germplasm data aggregators: Genesys
  5. 5. About Genesys • Developed by Bioversity International on behalf of – the System-wide Genetic Resources Programme of the CGIAR, – the Global Crop Diversity Trust and – the Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture. • Genesys was launched on 13 May 2011 URL: http://www.genesys-pgr.org/
  6. 6. Data aggregation 1. SINGER (Systems-Wide Information Network for Genetic Resources) 2. EURISCO (European National Germplasm Inventories) 3. GRIN (Germplasm Resources Information Network) of USDA
  7. 7. Genesys data • Provides access to almost 2,5M germplasm accession in 356 institutions of 238 countries. – This covers about one third of the genebank accessions estimated to be held worldwide. • Contains over 11 million Characterization and Evaluation (C&E) records • Environmental data records for the over 600,000 geo-referenced sites where accessions were collected.
  8. 8. Metadata model used • Schema based on MCPD – Adopted by SINGER & EURISCO • Expanded to include Characterization & Evaluation data (C&E) – As used by GRIN and CGIAR genebanks
  9. 9. Germplasm data aggregators: EURISCO
  10. 10. About EURISCO • EURISCO: based on a European network of ex situ National Inventories (NIs) that makes the European plant genetic resources data available everywhere in the world. • Maintained by Bioversity International on behalf of the Secretariat of the European Cooperative Programme for Plant Genetic Resources (ECPGR) in collaboration with the National Focal Points for the National Inventories. URL: http://eurisco.ecpgr.org
  11. 11. Data aggregation 1. National Focal Points – the unique link between the EURISCO and the European National Inventories (NIs) and national documentation systems. 2. National Inventories – A number of European countries have established national PGR inventories that are available on the web.
  12. 12. EURISCO germplasm data • The EURISCO Catalogue contains passport data on more than 1.1M samples of crop diversity – representing >5,600 genera and >36,00 species (genus-species combinations including synonyms and spelling variants) – from 43 countries *as of May 2012
  13. 13. Metadata model used • Schema based on MCPD – Adopted by SINGER & EURISCO • Expanded to include Characterization & Evaluation data (C&E) – As used by GRIN and CGIAR genebanks
  14. 14. Germplasm data aggregators: Global Biodiversity Information Facility (GBIF)
  15. 15. About GBIF • An international open data infrastructure, funded by governments. • Operates through a network of nodes, coordinating the biodiversity information facilities of participant countries and organizations, collaborating with each other and the Secretariat URL: http://www.gbif.org
  16. 16. Data aggregation • Data aggregated from almost 750 data sources, including – – – – – – Laboratories Research centers Corporations Museums NGOs Universities
  17. 17. GBIF data
  18. 18. Metadata model used • Dataset level: GBIF Metadata Application Profile – http://www.gbif.org/resources/2559 • Data level: – Darwin Core extension for germplasm (DwC-G) – Ecological Metadata Language (EML) – MCPD / EURISCO descriptors – Others?
  19. 19. USDA Germplasm Resources Information Network (GRIN)
  20. 20. About GRIN • Developed by the U.S. Department of Agriculture / Agricultural Research Service • Aims to acquire, characterize, preserve, document, and distribute to scientists, germplasm of all lifeforms important for food and agricultural production. URL: http://www.ars-grin.gov/
  21. 21. Data aggregation • Data aggregated from more than thirty germplasm USDA / ARS data sources, including – Arctic and Subarctic Plant Gene Bank Research centers – Desert Legume Program – Forest Service National Seed Lab – Maize Genetic Stock Center – National Arid Land Plant Genetic Resources Unit
  22. 22. GRIN data • Data available though GRIN includes – Passport, – Characterization & Evaluation, – Inventory and – Distribution data • > 500,000 accessions (distinct varieties of plants) in the GRIN database. – Representing >10,000 species of plants
  23. 23. Metadata model used • Passport information – Crop independent – Own schema* • Crop descriptors** – Crop specific *http://www.ars-grin.gov/npgs/pcgrin/manual/genlinfo.htm ** http://www.ars-grin.gov/npgs/pcgrin/manual/concepts.htm
  24. 24. ECPGR Germplasm Data
  25. 25. ECPGR Germplasm Databases • European Cooperative Programme for Plant Genetic Resources (ECPGR) – founded in 1980 on the basis of the recommendations of • the United Nations Development Programme (UNDP), • the Food and Agriculture Organization of the United Nations (FAO) and • the Genebank Committee of the European Association for Research on Plant Breeding (EUCARPIA). URL: http://www.ecpgr.cgiar.org/germplasm_databases.html
  26. 26. ECPGR Data sources • 64 ECPGR Central Crop Databases have been established by individual institutes and the ECPGR Working Groups. • The databases hold passport data and to varying degrees, characterization and primary evaluation data of the major collections of the respective crops
  27. 27. ECPGR germplasm data • ECPGR offers Web access to specific crop and multicrop databases: 1. ECPGR Central Crop Databases and other Crop Databases ECPGR and other Central Crop Databases have been established through the initiative of individual institutes and of ECPGR Working Groups. The databases hold passport data and, to varying degrees, characterization and primary evaluation data of the major collections of the respective crops in Europe. 2. Germplasm Collecting Missions Database 3. International Multi-crop Databases 4. National Multi-crop Databases
  28. 28. Crop Genebank Knowledge Base
  29. 29. Crop Genebank Knowledge Base • An initiative of the System-wide Genetic Resources Programme (SGRP) of the Consultative Group on International Agricultural Research (CGIAR). • Developed as part of the World Bank funded project “Collective Action for the Rehabilitation of Global Public Goods in the CGIAR Genetic Resources System, Phase 2 (GPG 2)”. URL: http://cropgenebank.sgrp.cgiar.org
  30. 30. CGKB data • A user-friendly online access to procedures, standards and practices for managing clonally propagated and seed crops held in genebanks. • Best practices in the framework of a learning platform. • Links to other related information and training resources. • A mechanism to update the existing best practices for crop management in genebanks and to develop best practices for additional crops. • Build capacity of genebank curators and technicians.
  31. 31. European Genebank Integrated System (AEGIS)
  32. 32. European Genebank Integrated System • Developed by the European Cooperative Programme for Plant Genetic Resources (ECPGR) • Supports the coordination of plant genetic resources for food and agriculture (PGRFA) URL: http://cropgenebank.sgrp.cgiar.org
  33. 33. AEGIS data • The European Collection – operated as a virtual European genebank, – composed of European Accessions conserved for the long-term by the AEGIS Associate Members on behalf of the ECPGR Member countries and being available for use or conservation only for the purposes of research, breeding and training for food and agriculture.
  34. 34. NordGen - Nordic Genetic Resource Center
  35. 35. NordGen • Nordic organization supporting the coordination of Nordic plant genetic resources for food and agriculture (PGRFA) • Joint initiative of all Nordic countries – Denmark, – Finland, – Iceland, – Norway, – Sweden URL: http://www.nordgen.org
  36. 36. NordGen SESTO • SESTO Genebank Documentation System – A genebank management tool developed by the Nordic Gene Bank (today Nordic Genetic Resource Center, NordGen). – Developed into a more generic PGR information system – Adopted for management and presentation of data from other genebanks in other parts of the world.
  37. 37. NordGen Data • Information available for: – Trait Datasets – Trait Descriptors – Germplasm accessions – Observations
  38. 38. Conclusions
  39. 39. Conclusions (1/2) • Germplasm data available from several sources – Global aggregators – National Inventories/aggregators – Individual data sources • Different metadata used in each case – Highlights the need for harmonization of standards – Standard vocabularies will allow linked data approach
  40. 40. Conclusions (2/2) • Aggregation of metadata facilitates harmonization – Application of a common standard for several data sources • Exposure of metadata as linked data per aggregator
  41. 41. Next steps • Complete pending mapping between existing standards – Work of bioinformatics experts • Define common vocabularies – Work of germplasm experts • Deploy a linked germplasm data framework – agINFRA could help with that
  42. 42. References • Geser, Guntram (2012) “agINFRA Dossier on Germplasm information”. Available online at: http://wiki.aginfra.eu/index.php/Germplasm_Working_Group • Websites of data sources mentioned in the presentation
  43. 43. Source: http://verastic.com/social/why-do-people-not-say-thank-you.html Contact me: vprot@agroknow.gr

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