The document details a genetic resources global information systems training course held in January 2009, which covered documentation, data standards, and data exchange for germplasm catalogues from various sources including Eurisco, Singer, and USDA-GRIN. It emphasizes the conservation and availability of unique genetic accessions for breeding and research, particularly in Europe, and discusses ongoing projects and initiatives aimed at improving data management and exchanges on a global scale. The document also outlines the role of organizations like Bioversity International and Nordic Genetic Resource Center in supporting genetic resource efforts.

1. Cover slide Documentation of Genetic Resources Global Information Systems CAC Training Course January 29, 2009 NordGen, Alnarp Dag Terje Filip Endresen Nordic Genetic Resource Center/ Bioversity International

2. TOPICS Documentation of genetic resources: Information Systems Data standards Data exchange Distributed data network

3. Global PGR Information Systems

4. Germplasm catalogues The three large germplasm catalogues are indexed by the GBIF data portal EURISCO is the data catalogue of the European genebanks ( more than 1 000 000 accessions ) SINGER is the portal to the international CGIAR collections ( more than 650 000 accessions ) USDA-GRIN is the portal to the USDA ARS National Germplasm Repositories of the USA ( more than 400 000 accessions )

5. ECPGR (AEGIS, ECCDB, EURISCO) A European Genebank Integrated System (AEGIS) Sharing of responsibilities ( Most Appropriate Accession ; common agreed quality standards for e x situ conservation ). Conservation of the genetically unique and important accessions for Europe and making them available for breeding and research . F our model crops : Allium , Avena , Brassica and Prunus species . Membership in AEGIS is open to all European countries (ECPGR) . EURISCO and the Central Crop Databases play a key role in the information management .

6. ECPGR Central Crop Databases

7. ECPGR Central Crop Databases

8. EURISCO [ http://eurisco.ecpgr.org/ ] EURISCO data catalogue of the European genebanks (more than 1 0 00 000 accessions from 35 European countries) EURISCO holds accession level data on 1 300 genera and 8 500 species. EURISCO was released in September 2003 as a result of the EU funded EPGRIS project. EURISCO is hosted by Bioversity International on behalf of the ECPGR.

9. EURISCO (new layout)

10. Data flow from genebanks to EURISCO and ECCDBs

11. EPGRIS3 [ http://www.epgris3.eu/ ] EPGRIS3 is a volunteer self-funded follow up on the EU funded EPGRIS project. EPGRIS3 is about improving the data exchange of European genebank datasets and to further develop the IT infrastructure on genetic resources in Europe.

12. EPGRIS3 Wiki Environment A EPGRIS3 Wiki environment is hosted by NordGen. Please register and contribute to the discussions. [ http://wwwdev.ngb.se/epgris3/ ] Please make contact with one of the EPGRIS3 contact persons if you want to contribute to the EPGRIS3 project. [ http://www.epgris3.eu/ EPGRIS3contacts.htm ]

13. SINGER [ http://singer.grinfo.net/ ] The System-wide Information Network for Genetic Resources (SINGER) . More than 650 000 accessions from the 12 international CGIAR organizations. SINGER is hosted by Bioversity International on behalf of the CGIAR.

14. CGIAR [ http://www.cgiar.org/ ] AVRDC - The World Vegetable Center Bioversity - Bioversity International CIAT - Centro Internacional de Agricultura Tropical CIMMYT - Ce ntro Internacional de Mejoramiento de Maiz y Trigo CIP - C entro Internacional de la Papa ICARDA - International Center for Agricultural Research in the Dry Areas ICRAF - The World Agroforestry Centre ICRISAT - International Crops Research Institute for the Semi-Arid Tropics IITA - International Institute of Tropical Agriculture ILRI - International Livestock Research Institute IRRI - International Rice Research Institute WARDA - The Africa Rice Center

15. GCP [ http://www.generationcp.org/ ] GCP G eneration C hallenge P rogramme. The GCP Mission: To use advanced genomics science and plant genetic diversity to overcome complex agricultural bottlenecks that condemn millions of the world’s neediest people to a future of poverty and hunger . The GCP Vision: A future where plant breeders have the tools to breed crops in marginal environments with greater efficiency and accuracy for the benefit of the resource-poor farmers and their families.

16. NordGen [ http://www.nordgen.org/ ] The Nordic Genetic Resource Center (NordGen) was established in January 2008. NordGen replaces the former institute Nordic Gene Bank (NGB) established in 1979. NordGen is the joint regional genetic resource center for all the 5 Nordic countries: Denmark, Finland, Iceland, Norway and Sweden. The NordGen reports to the Nordic Council of Ministers [ http://www.norden.org ]. The mandate of the NordGen is conservation and utilization of Nordic Genetic Resources.

17. Regional Programs on Genetic Resources SEEDNet, South East European Development Network on Plant Genetic Resources was established in 2004. [ http://seednet.geminova.net/ ] SADC, Southern African Development Community program on genetic resources was started in 1989. [ http://www.spgrc.org/ ] USDA GRIN, Germplasm Resources Information Network of the US. [ http://www.ars-grin.gov/ ] … and more

18. GBIF Global Biodiversity Information Facility

19. GBIF Data Portal GBIF [ http:// data .gbif.org/ ]

20. GBIF PGR Network 2 [ http://data.gbif.org/datasets/network/2 ]

21. GBIF NordGen [ http:// data .gbif.org/ ]

22. GBIF SINGER [ http:// data .gbif.org/ ]

23. GBIF USDA

24. FAO WIEWS

25. FAO WIEWS [ http://apps3.fao.org/wiews / ]

26. FAO WIEWS, GPA [ http://www.pgrfa.org/gpa/ ] Leipzig Declaration 1996, 150 countries [ http://www.globalplanofaction.org/ ]

27. Data Standards

28. Crop Descriptors The crop descriptor lists from Bioversity International provide global standards for characterization and evaluation data on crop genetic resources. The MCPD (Multi Crop Passport Descriptor List) provides a global standard for "passport data" across the crops. The MCPD descriptor list is compatible with the TDWG standard: ABCD 2.06.

29. Accession level, Data Standards Multi Crop Passport (MCPD) [http://www.bioversityinternational.org/publications/pubfile.asp?id_pub=124] Darwin Core (DwC v2) [http://wiki.tdwg.org/twiki/bin/view/DarwinCore/] Access to Biological Collection Data (ABCD 2.06) [http://wiki.tdwg.org/twiki/bin/view/ABCD] Generation Challenge Programme (GCP Passport v1.05) [http://gcpcr.grinfo.net/include/webservices/schema-documentation.php]

30. W3C :: RDF Resource Description Framework Scenario: You have a dataset of genebank accessions with pointers to the source datasets of the holding genebanks. You produce phenotypic evaluation data on accessions in this dataset. You find evaluation data from other sources on some of the accessions in your dataset. Some of the evaluation data are produced in areas of different day length, rainfall, soils… Some of the accessions in your dataset originate from areas of higher population densities other accessions originate from more natural habitats. Unfortunately most of the different sources of information is located on different web sites and it is difficult to bring the information together. You would need to go through more or less the same process as other researchers in many domains of gathering heterogeneous data from multiple sources, combining and analysing it. This is the challenge that faces the web as a whole and is being addressed by the Semantic Web project. RDFs can assist you to relate information from different sources. A RDF triplet looks like this: subject-predicate-object <rdf:Description rdf:about=&quot;http://www.example.org/index.html&quot;> <dc:creator>John Smith</dc:creator> </rdf:Description> anytime approximate case study diagnosis inconsistent kads banana apples stem color knowledge based systems knowledge level knowledge management knowledge representation LSID accession number GUID unitID ontology owl parametric design Full Scientific Name peer to peer systems problem solving landrace traditional cultivar 300 methods rdf rdf WEB2 ABCD SDD semantic web semantics specification languages web based web ontology INSTCODE plant genetic resources germplasm agricultural traits Aegilops

31. Life Science IDentifiers LSID is a digital name tag. LSIDs are GUIDs, Global Unique Identifiers. [http://lsid.sourceforge.net/] Structure urn:lsid: authority : namespace : object : revision Example (fictive) urn:lsid:eurisco.org:accession:H451269 The LSID concept introduces a straightforward approach to naming and identifying data resources stored in multiple, distributed data stores . LSID define s a simple, common way to identify and access biologically significant data LSID provides a naming standard to support interoperability. Developed by OMG-LSR and W3C, implemented by IBM. W3C :: LSID

32. Taxon References http://www.catalogueoflife.org http://www.itis.gov/

33. Biodiversity data exchange tools

36. Test resource with client form: http://localhost/tapirlink/tapir_client.php The XML Client form is very illustrative for understanding exactly how the wrapper software works!

37. Data Provider Software PyWrapper v3, based on the BioCASE Python software. [ http://www.pywrapper.org/ ] [ http://www.biocase.org/ ] DiGIR, Di stributed G eneric I nformation R etrieval. [ http://digir.net ] TapirLink [ http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink ] TapirDotNet [ http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirDotNET ]

38. Distributed BioCASE/PyWrapper network

40. Example of a service request All exchanged data is formatted with XML tags.

41. Example of a service response

42. Data portal and decentralized data networks with web services

43. Data warehouse model

44. EURISCO (Europe) NordGen (Northern Europe) IPK Gatersleben (Germany) IHAR (Poland) (Other European gene banks...) SINGER (CGIAR) (CGIAR International Future Harvest gene banks...) USDA GRIN (USA) (USDA ARS National Germplasm Repositories...) WUR CGN (Netherlands) GBIF (Global Biodiversity Information Facility) USER ALIS (Accession Level Information System) Web Services MCPD Svalbard Global Seed Vault (Safe Backup)

45. Germplasm data indexing tools We have recently built data indexing tools for access to gene bank datasets provided with the BioCASE/PyWrapper. This is planned to build a Global Accession Level Information System (ALIS). In cooperation with GBIF, which themselves index basic biodiversity data from a similar approach. [ http://chm.grinfo.net/ ]

46. [ http://wwwdev.ngb.se/portal/ ]

47. Crop Wild Relatives ARM LKA BOL MDG UZB National Datasets are shared with the central CWR data index. The national datasets as well as access to other International datasets are provided from the CWR data portal. EURISCO SINGER [ http://www.cropwildrelatives.org ]

48. Taxonomy level metadata The Taxon and Country pages provides access to the relevant external datasets.

49. Country level metadata

50. Participation and the sharing of your institute datasets with global and national biodiversity projects is important for your public and scientific visibility, promoting the use (usefulness) of your data and ultimately for the continued funding of your institutional activities.

51. Bioversity International [http://www.bioversityinternational.org] GBIF, Global Biodiversity Information Facility [http://www.gbif.org] BioCASE , The Biological Collection Access Service for Europe. [http://www.biocase.org] TDWG , Biodiversity Information Standards [http://www.tdwg.org]

52. Thank you for listening!