Regional GBIF NODES meeting of Europe in March 2010. Presentation of current activities from the NordGen NODE. Implementations of the GBIF IPT toolkit for genebanks in Europe. Upgrade for selected genebanks from the BioCASE publishing toolkit to the IPT. First step of a scheduled larger implementation planned to start in 2011 as part of the EuroGeneBank application pending EU funding decision. NordGen IPT EURISCO

1. European GBIF Nodes Meeting 2010, March 10th-12th Alicante, Spain Dag Endresen, Nordiv Genetic Resources Center, NordGen GBIF IPT installations for EURISCO GBIF Tools and Darwin Core extension for germplasm Cartoon by Sasha Kopf (Creative Commons)

3. Overview of the project

4. Darwin Core extension for germplasm

5. GBIF informatics tools

6. Integrated Publishing Toolkit (IPT)

7. IPT installations for EURISCO

9. From the contract between NordGen and GBIF: “... a feasibility study aimed at demonstrating the practical implementation of the GBIF decentralised architecture strategy and in particular in the context of the EURISCO Network.” “... focused on the adoption of the IPT by selected gene banks in Europe, the publishing of richer content using the Darwin Core germplasm extension and the indexing of these published resources by the EURISCO platform.” “... implemented in the context of EURISCO and therefore in close collaboration with the EURISCO Coordinator.”

12. a flexible framework to maximize re-usability The Darwin Core can be extended by adding new terms to share additional information. 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/

13. DwC star schema model

15. Maintained by gene banks worldwide

16. Additional terms to describe germplasm samples

17. Includes the new terms for crop trait experiments developed as part of the European EPGRIS3 project

18. Includes a few additional terms for new international crop treaty regulationshttp://code.google.com/p/darwincore-germplasmhttp://rs.nordgen.org/dwc

19. DwC Germplasm (1)

20. DwC Germplasm (2)

21. DwC Germplasm (3)

22. DwC Germplasm (4)

23. DwC Germplasm (5)

25. Seed cleaning

26. Seed germination testingConservationStatus Suggested by ENSCONET - threat status for populations in situ

27. Mapping of DwC-G terms to the MCPD descriptors

28. Mapping of DwC-G terms to the MCPD descriptors (continued)

29. MCPD -> ABCD 2.06 (2004) National Inventory Code Institute Code Accession Number Collecting Number Collecting Institute Code Genus Species Species Authority „Subtaxa“ „Subtaxa“ Authority Common Crop Name Accession Name Acquisition Date 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/Acquisition Source Donor Institute Code Donor Accession Number Other Identification (Number) associated with the accession Location of Safety Duplicates Type of Germplasm Storage Remarks Decoded Collecting Institute Decoded Breeding Institute Decoded Donor Institute Decoded Safety Duplication Location Accession URL Helmut Knüpffer IPK Gatersleben Descriptors marked red did not match the earlier versions of ABCD  ABCD was extended by a PGR section [W. Berendsohn, H. Knüpffer] Walter Berendsohn BGBM http://www.ecpgr.cgiar.org/epgris/Tech_papers/EURISCO_Descriptors.pdf

30. Home: http://code.google.com/p/gbif-providertoolkit/ Primary developers: Markus Döring, Tim Robertson, John Wieczorek Source code: Java Released: 2009 DEMO at http://ipt.gbif.org/ Genebank Example at http://ipt.nordgen.org/ipt/

31. Integrated Publishing Toolkit (IPT) A tool in support of data publishers. A simple and straightforward 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.

33. Apache Tomcat is recommended (1 GB RAM+)

34. GBIF IPT is provided as a WAR archive (for easy deployment)

35. GeoServer is included for web mapping (OGC Compliant, WFS, WMS, etc)

36. H2 Embedded Java Database (with JDBC interface and web console)

38. TAPIR

39. DwC Archive

40. OGC (WFS, WMS, Web Mapping)

42. Simple text based format

43. Zipped single file archiveGermplasm.txt http://code.google.com/p/gbif-ecat/wiki/DwCArchive

47. Multilingual

48. Has a user management feature based on roles, which allows for multiple data managers to share a common instance

49. Manages multiple data sources

50. Several upload options: relational database management systems or data files

51. Public web interface allows for data browsing and full text search

53. The IPT user interface includes the germplasm extension

54. XML interface includes thegermplasm extension

55. The Harvesting and Indexing Toolkit (HIT) Addresses the need of Nodes managers, to aggregate indexes of published primary biodiversity data. Aims to ease the complexity of heterogeneous networks of data publishers, by shielding the end-user from the complexities of the different protocols.

56. Biodiversity Resources Discovery System (GBRDS) A Yellow Page reference of Biodiversity resources. The IPT and HIT instances installed in the course of this project will be registered in the GBRDS. Any biodiversity organisation should be able to register their resources and services into the GBRDS and contribute to the discovery services.

58. Upgrade of the Integrated Publishing Toolkit (IPT) with the genebank extension and develop associated documentation.

59. Install and test the IPT installation in various genebanks in Europe that, as far as possible, are also EURISCO/ECPGR partners.

60. Test the registration of IPT installation through the GBIF Global Biodiversity Resources Discovery System (GBRDS).

61. Test the Harvesting and Indexing Toolkit (HIT) installation for the EURISCO platform.

62. Install an IPT instance on the EURISCO platform and synchronize with GBIF central Index.

64. EURISCO / Bioversity-HQ (Italy)

65. Bioversity-Montpellier (France)

66. IPK Gatersleben (Germany)

67. WUR CGN (The Netherlands)

68. CRI (Czech Republic)

69. VIR (Russia)

70. Balkan countries (Albania, Bosnia, Croatia, Macedonia, Serbia, Romania)

72. The National Inventory (NI) endorse all national gene banks (and eventually individual accessions) for EURISCO.

73. ECPGR Crop databases can access passport data from EURISCO and additional crop specific data from the genebank IPT interface.

76. TDWG, Biodiversity Information Standards http://www.tdwg.org