EURISCO needs and priorities, at CGIAR ICT-KM Workshop, IPGRI, Rome (2005)

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European genebanks, EURISCO and NGB. Overview of needs and priorities. CGIAR ICT-KM training workshop on information interoperability, 14th June 2005, IPGRI Rome Italy. Dag Endresen (Nordic Gene …

European genebanks, EURISCO and NGB. Overview of needs and priorities. CGIAR ICT-KM training workshop on information interoperability, 14th June 2005, IPGRI Rome Italy. Dag Endresen (Nordic Gene Bank).

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  • * Photo: Field of wheat at Alnarp. Photographer Dag Terje Endresen (NGB Picture Archive, image 002981) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=002981] * Red beet, Beta vulgaris L. at the vegetable counter. Photographer Dag Terje Endresen (NGB Picture Archive, image 002995) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=002995] * Photo: Field trip during PGR Forum Workshop 5 in September 2004 on the Azores. Visit to a wine yard. Photographer Dag Terje Endresen (NGB Picture Archive, image 003870) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=003870]
  • * Photo: Asparagus officinalis L. in the vegetable counter. Photographer Dag Terje Endresen (NGB Picture Archive, image 002992) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=002992]
  • * Field of wheat at Alnarp. Photographer Dag Terje Endresen (NGB Picture Archive, image 002982) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=002982]
  • Illustration: PGR data flow in Europe by Frank Begemann (ZADI) for ECP/GR Documentation and Information Network.
  • Nordic and Baltic seed collections and clonal archives with vegetatively preseved genetic resources [http://tor.ngb.se/Material/Clonal.php]
  • * Illustration: Dag Terje Filip Endresen (NGB Picture Archive, image 003890) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=003890] * Photo: Latvian genebank, drying room. Salaspils outside Riga. Bent Skovmand and Isaak Rashal. Photographer Dag Terje Endresen (NGB Picture Archive, image 002402) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=002402]
  • * Spiders-web, photographer: Ian-Britton [http://www.freefoto.com/preview.jsp?id=01-17-6&k=Spiders+Web] * Copyright statement “feel free to use any of the images on the site if you are a private individual and your use is not commercial” [http://www.freefoto.com/browse.jsp?id=99-5-0]
  • * Illustration: Tapir - © 1999-2005 www.barrysclipart.com (Licence “Feel free to use Barrys Clipart Server content in personal/ non profit projects to create webpages…”) [http://www.barrysclipart.com/barrysclipart.com/showphoto.php?photo=13376&papass=&sort=1&thecat=149]
  • * Spiders-web, photographer: Ian-Britton [http://www.freefoto.com/preview.jsp?id=01-17-3&k=Spiders+Web] [http://www.freefoto.com/preview.jsp?id=01-17-4&k=Spiders+Web] Copyright statement “feel free to use any of the images on the site if you are a private individual and your use is not commercial” [http://www.freefoto.com/browse.jsp?id=99-5-0] * Large orb weaver spider sitting on web. [http://www.pixelperfectdigital.com/index.php?action=showpic&cat=17&pic=2160] Terms of use: [ http://www.pixelperfectdigital.com/terms_of_use.txt] © 2005 Pixel Perfect Digital, Inc.
  • * Peas in the drying room. Pisum sativum. Photographer Dag Terje Endresen and Vijal Jadav (NGB Picture Archive, image 002968) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=002968] * Seeds of Barley in the drying room. Photographer Dag Terje Endresen and Vijal Jadav (NGB Picture Archive, image 002965) [http://www.ngb.se/sesto/index.php?scp=ngb&thm=divpic&mod=det&id=002965]
  • * SINGER - The System-wide Information Network for Genetic Resources (SINGER) is an information exchange network of the Future Harvest Centres of the Consultative Group on International Agricultural Research (CGIAR) and associated partners. [ http://singer.grinfo.net/] * European Plant Genetic Resources Search Catalogue with passport data on ex situ collections maintained in Europe. [ http://eurisco.ecpgr.org/] * USDA-Grin - The Germplasm Resources Information Network (GRIN) web server provides germplasm information about plants, animals, microbes and invertebrates. This program is within the U.S. Department of Agriculture's Agricultural Research Service. [http://www.ars-grin.gov/npgs/]
  • Weed control in soybeans. Photo by Keith Weller. [http://www.ars.usda.gov/is/graphics/photos/k5197-3.htm] Sugarcane harvested and loaded into high dump trailers in Bunkie, Louisiana. Photo by David Nance [http://www.ars.usda.gov/is/graphics/photos/k7089-3.htm]

Transcript

  • 1. European Gene Banks, EURISCO and NGB Overview of Needs and Priorities Training Workshop on interoperability June 14, 2005 – IPGRI, Rome Dag Terje Filip Endresen – The Nordic Gene Bank
  • 2. TOPICS for this presentation
    • European Gene Banks (ECP/GR)
    • European Central crop databases
    • EURISCO
    • Nordic Gene banks
    • Conclusions
  • 3. EURISCO and GBIF
    • I will try to show that:
    • The objective and mode of operation of EURISCO, (SINGER) and GBIF overlaps.
    • The EURISCO network of National Inventories (NIs) is similar to the SINGER network of CGIAR Centers and to the GBIF network of national Nodes.
    • The EURISCO (and SINGER) network infrastructure can be built based on GBIF and TDWG standards and protocols.
  • 4. E uropean C ooperative P rogramme for Crop G enetic R esources Networks
    • More than 50 „ Central Crop Databases“ in Europe > 20 years (Wheat, Potato, Barley etc.)
    • EURISCO – central inventory of plant genetic resources in Europe.
      • EU project EPGRIS (1999-2003)
      • 42 national programs (Europe)
      • at present 920,147 accessions
      • approximately 50% of the estimated accessions in European genebanks.
    ECP/GR
  • 5. European PGR Network model
    • The accession (passport) data is curated and shared from the local genebank node
    • Data to EURISCO is endorsed by the NI
    • The EURISCO data portal node provides access to the data for the ECCDBs
    • There is no data network without a parallel human network.
    Data Portal ECCDB Data Node Gene bank Participant Node NI Portal Node EURISCO Data flow
  • 6. PGR Data Flow in Europe Frank Begemann, ECP/GR *At the discretion of the National Focal Point ** Data flow for char. & evaluation data to be discussed
  • 7. Where we are today (Europe)...
    • Dataflow from gene bank to EURISCO and ECCDB as flat files, tab-separated MCPD.
    MCPD eMCPD EURISCO Central Data warehouse MCPD +crop specific descriptors Central Crop Database ECCDB Gene Bank Databases Central Data ware house model N ational I nventory
  • 8. Future decentralized model...
    • Dataflow from gene bank to EURISCO and ECCDB through decentralized web services .
    XML Web Service layer (agreed standards and data provider software) Central Crop Portal EURISCO Portal GBIF Portal etc... XML XML XML BioCASE Portal XML XML etc... Gene Bank Database [1] N ational I nventory Portal XML Gene Bank Database [2]
  • 9. Real world, mixed model...
    • Dataflow from gene bank to EURISCO and ECCDB through decentralized web services .
    N ational I nventory XML Central Crop Database ECCDB Web Service layer (agreed standards and data provider software) XML XML XML ECCDB Portal EURISCO Portal GBIF Portal etc... XML XML XML BioCASE Portal XML EURISCO database Gene Bank Database NI Portal XML Gene Bank Database Gene Bank Database Other Database Gene Bank Database Other Database Other Datasource Gene Bank Database Other Datasource
  • 10. Nordic and Baltic PGR collaboration
    • NGB is coordinating the international regional network of Nordic and Baltic genebanks.
  • 11. Nordic Baltic Regional PGR network
    • SESTO is the common regional documentation platform for data management.
    • Improved data exchange models and network infrastructure is needed to develop this model further.
  • 12. EURISCO as a network of web services
    • EURISCO (& NGB) needs:
    • Data provider software
    • can we use BioCASE or DiGIR (BioMOBY??)
    • Data portal software
    • can we adopt the GBIF or BioCASE data portal software?
    • can we use the GBIF UDDI registry?
    • Network of people
    • we have the network of NIs from EPGRIS
    • we have the ECP/GR and the ECCDBs
    • Data standards
    • can we use ABCD, (Darwin Core 2)?
    • ABCD 2.0 is compatible with MCPD
  • 13. Choosing the data provider software
    • The new unified protocol specification TAPIR (implementation for BioCASE and DiGIR?)
    • Implement BioCASE , ABCD is compatible with MCPD and has a separate PGR sub-unit.
    • DiGIR use Darwin Core, where mapping to MCPD is incomplete (?)
  • 14. Choosing the data portal software
    • Develop a specific EURISCO UDDI registry or explore alternatives to use the GBIF UDDI registry
    • Adopt the GBIF portal software for EURISCO (based on Java and MySQL, free open source)
    • Adopt the BioCASE portal software (based on Python, free open source)
  • 15. European Genebanks as GBIF providers
    • IPK Gatersleben, Germany
    • 109 711 records (BioCASE) August 2004
    • National Centre for Plant Genetic Resources, IHAR, Poland
    • 40 459 records (DiGIR) March 2004
    • The Nordic Gene Bank, NGB
    • 26 868 records (BioCASE, DiGIR) March 2004
    • EURISCO (2005 ...??)
  • 16. ENBI E uropean N etwork for B iodiversity I nformation
    • ENBI is an European contribution to the Global Biodiversity Information Facility (GBIF).
    • ENBI is a thematic network supported by the European Commission under the fifth Framework Programme and contributing to the "Energy, environment and sustainable development" programme. Contract no EVK2-CT-2002-20020.
    • EPGRIS and EURISCO are represented in ENBI
    • IPGRI is a member of ENBI (wp6)
    • BioCASE is represented in the membership of ENBI
    • [http://www.enbi.info]
  • 17. EPGRIS-2
    • EPGRIS-2 project under development, expected to start in 2006.
    • WP1 Coordination
    • WP2 Data standards
    • WP3 Network infrastructure
    • WP4 Capacity development
    • WP5 Pilot Crop portals
    • WP6 GIS visualization
    • WP7 Taxonomy
  • 18. Major Global Crop collections
    • EURISCO is an inventory of 926,231 accessions from European Gene Banks
    • The CGIAR Gene Banks hold over 530,000 samples of wild and domesticated crops in public trust.
    • USDA-Grin holds 464,389 accessions.
    Accessions in EURISCO (926,231) Accessions in SINGER (524,466)
  • 19. Conclusions
    • To build the genetic resources infrastructure on GBIF technology and global biodiversity standards.
    • All European Gene banks to join GBIF through EURISCO .
    • Will the CGIAR Future Harvest Centers join GBIF through SINGER ?
    • Will USDA-GRIN join GBIF?
    • Will BioMOBY join GBIF??
  • 20.
    • Thank you for listening!