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EURISCO and GBIF IPT, at the Vavilov Institute in St Petersburg (27 April 2010)
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EURISCO and GBIF IPT, at the Vavilov Institute in St Petersburg (27 April 2010)

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Visit to the NI Vavilov Institute for Plant Industry (VIR) in April 2010. Installation of the GBIF IPT toolkit for data publishing as a test upgrade for the EURISCO data infrastructure of European …

Visit to the NI Vavilov Institute for Plant Industry (VIR) in April 2010. Installation of the GBIF IPT toolkit for data publishing as a test upgrade for the EURISCO data infrastructure of European genebanks.

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  • IMAGE: http://blog.tapirtype.com/cartoons/ [Creative Commons License: http://creativecommons.org/licenses/by-nc-sa/3.0/us/]
  • Darwin core
  • Technology overview – IPT role
  • PPT: Nick King and Vishwas Chavan, Albuquerque, 2-7 Aug. 2009
  • Transcript

    • 1. Web service demo for EURISCO
      GBIF Tools and Darwin Core extension for germplasm
      N.I. Vavilov Research Institute of Plant Industry (VIR), April 26th – 29th 2010, St Petersburg, Russian Federation
      Dag Endresen, Jonas Nordling, Nordic Genetic Resources Center (NordGen)
    • 2. Topics for this session
      • Web service installations for EURISCO
      • 3. Overview of the current project
      • 4. Darwin Core and the extension for germplasm
      • 5. GBIF informatics tools
      • 6. Integrated Publishing Toolkit (IPT)
      • 7. Distributed datasets
      2
    • 8. Possible Upgraded PGR Network Model
      • The gene bank dataset is shared from the holding gene bank.
      • 9. The National Inventory (NI) endorse all national gene banks (and eventually individual accessions) for EURISCO.
      • 10. ECPGR Crop databases can access passport data from EURISCO and additional crop specific data from the genebank IPT interface.
      • 11. Standard data sharing tools ensure that the genebank dataset is available to other relevant decentralized thematic, regional or global networks.
      3
    • 12. Objectives of the EURISCO demo project
      • Evaluate the GBIF decentralized architecture
      • 13. Install the IPT installation for 8 genebanks in Europe that, as far as possible, are also EURISCO/ECPGR partners.
      • 14. Test the registration of IPT installation through the GBIF registry
      Global Biodiversity Resources Discovery System (GBRDS).
      • Test the Harvesting and Indexing Toolkit (HIT) installation for the EURISCO platform (Bioversity HQ, Rome).
      • 15. Project runs until 20 December 2010.
      4
    • 16. 2010 : IPT installations for EURISCO
      • EURISCO
      • 17. NordGen (Nordic)
      • 18. Bioversity-Montpellier (France)
      • 19. IPK Gatersleben (Germany)
      • 20. BLE (Germany)
      • 21. WUR CGN (The Netherlands)
      • 22. CRI (Czech Republic)
      • 23. VIR (Russian Federation)
      • 24. SeedNET (Balkan)
      • 25. Baltic (Estonia, Latvia, Lithuania)
      5
    • 26. 2005 : BioCASE demo
      http://chm.grinfo.net/
      6
    • 27. Potential of the GBIF technology
      Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.
      The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community (TDWG, GBIF).
      http://data.gbif.org/datasets/network/2
      7
    • 28. Darwin Core
      The purpose of DwC terms is to facilitate data sharing
      • a well-defined standard core vocabulary
      • 29. a flexible framework to maximize re-usability
      The Darwin Core can be extended by adding new terms to share additional information.
      Approved as TDWG standard 2009
      “The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information.”
      http://rs.tdwg.org/dwc/
      8
    • 30. DwC extension for germplasm
      DwC Germplasm : DRAFT 0.1 : August 26, 2009
      • “MCPD in Darwin Core”
      • 31. Maintained by gene banks worldwide
      • 32. Additional terms to describe germplasm samples
      • 33. Includes the new terms for crop trait experiments developed as part of the European EPGRIS3 project
      • 34. Includes a few additional terms for new international crop treaty regulations
      http://code.google.com/p/darwincore-germplasmhttp://rs.nordgen.org/dwc
      9
    • 35. Mapping of DwC-G terms to the MCPD descriptors (EURISCO data exchange format)
      10
    • 36. Mapping of DwC-G terms to the MCPD descriptors (continued)
      11
    • 37. MCPD -> ABCD 2.06 (2004) for BioCASE
      National Inventory Code
      Institute Code
      AccessionNumber
      CollectingNumber
      Collecting Institute Code
      Genus
      Species
      SpeciesAuthority
      „Subtaxa“
      „Subtaxa“ Authority
      Common Crop Name
      Accession Name
      Acquisition Date
      Donor Institute Code
      DonorAccessionNumber
      OtherIdentification (Number) associatedwiththeaccession
      Location of SafetyDuplicates
      Type of Germplasm Storage
      Remarks
      DecodedCollecting Institute
      DecodedBreeding Institute
      DecodedDonor Institute
      DecodedSafetyDuplicationLocation
      Accession URL
      Country of Origin
      Location of Collection Site
      Latitude of CS
      Longitude of CS
      Elevation of CS
      Collecting Date of Sample
      Breeding Institute Code
      Biological Status of Accession
      Ancestral Data
      Collecting/AcquisitionSource
      Helmut Knüpffer
      IPK Gatersleben
      http://www.ecpgr.cgiar.org/epgris/Tech_papers/EURISCO_Descriptors.pdf
      Walter Berendsohn
      BGBM
      12
    • 38. GBIF Informatics Suite
      • GBIF tools to empower decentralized thematic or regional networks
      • 39. Darwin Core extension for germplasm makes these tools usable for crop gene banks.
      13
    • 40. Integrated Publishing Toolkit (IPT)
      A tool for data publishers.
      A simple mechanism to share primary biodiversity data following the Darwin Core standard.
      Open source, Java based web application.
      Provides a local tool for data quality assessment, etc.
      14
    • 41.
      • Embeds its own database
      • 42. Multilingual
      • 43. Has a user management feature based on roles, which allows for multiple data managers to share a common instance
      • 44. Manages multiple data sources
      • 45. Several upload options: relational database management systems or data files
      • 46. Public web interface allows for data browsing and full text search
      • 47. Customised detail pages
      15
    • 48. The IPT user interface includes the germplasm extension
      16
    • 49. XML interface includes thegermplasm extension
      17
    • 50. European ECPGR Crop Databases
      European EURISCO Catalog
      VIR (RUS001)
      Passport data
      Global Crop Registries
      VIR (RUS001)
      Crop departments
      18
    • 51. Same dataset available from multiple information systems...
      ?!
      VIR Crop
      dataset
      ECPGR Crop Databases
      VIR (RUS001)
      Passport data
      EURISCO
      Global Crop Registries
      19
    • 52. Resolvable persistent identifiers can direct the user to the publisher of the primary dataset (official original dataset)
      VIR Crop
      dataset
      ECPGR Crop Databases
      VIR (RUS001)
      Passport data
      EURISCO
      Global Crop Registries
      20
    • 53. Persistent Identifier
      The Persistent Identifier (PI) is a digital name tag
      Also called Global Unique Identifiers (GUID)
      Life Science Identifiers (LSID) is one example
      Digital Object Identifier (doi) is another example
      The Persistent Identifier concept for to naming and identification of data resources stored in multiple, distributed data stores.
      Effective identification of data objects is essential for linking the world’s biodiversity data.
      21
    • 54. Moving towards…global integration of information
      Genebank datasets
      Spatial data
      Threatened species
      Crop standards
      Migratory species
      Legislation and regulations etc.
      Crop collections in Europe
      Global crop system
      22
      Global crop collections
    • 55. Special thanks to:
      • GBIF, Global Biodiversity Information Facility http://www.gbif.org
      • 56. TDWG, Biodiversity Information Standards http://www.tdwg.org
      • 57. Bioversity International
      http://www.bioversityinternational.org
      Things can happen in a band, or any type of collaboration, that would not otherwise happen. (Jim Coleman, Musician)