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.

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)

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 datasets2

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

13. Install the IPT installation for 8 genebanks in Europe that, as far as possible, are also EURISCO/ECPGR partners.

15. Project runs until 20 December 2010.4

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

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

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 regulationshttp://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

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

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 pages15

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

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)