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 genebanks.

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  • IMAGE: [Creative Commons License:]
  • Darwin core
  • Technology overview – IPT role
  • PPT: Nick King and Vishwas Chavan, Albuquerque, 2-7 Aug. 2009
  • EURISCO and GBIF IPT, at the Vavilov Institute in St Petersburg (27 April 2010)

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