GIGA TAG meeting at Bioversity International, Rome, Italy 18th May 2009. Data exchange alternatives for the Global Information on Germplasm Accessions (GIGA) project. Dag Endresen (Bioversity/NordGen).

1. Data exchange alternatives Global Information on Germplasm Accessions (GIGA, ALIS) 2nd GIGA Technical Advisory Group Meeting Dag Terje Filip Endresen, Nordic Genetic Resources Center, NordGen (Sweden)

2. Data exchange 2 Cartoon by Sasha Kopf (Creative Commons)

3. Data Exchange Format MCPD (1997) Multi Crop Passport Descriptors Darwin Core (2001) ** New version up for revision at TDWG2009 http://rs.tdwg.org/dwc/index.htm ABCD (2001) Access to Biological Collections Data http://wiki.tdwg.org/twiki/bin/view/ABCD GCP Passport (2005) http://www.generationcp.org Ontology (including all above) perhaps develop a new GIGA ontology 3

4. Data Provider Software BioMOBY (2001) http://biomoby.org DiGIR (2002, not active) http://digir.sourceforge.net BioCASE (2003, PyWrapper v2) http://www.biocase.org EURISCO (2003, tab delimited text) http://eurisco.ecpgr.org PyWrapper 3 (2006, not active) http://trac.pywrapper.org TapirLink (2007) http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink GBIF Provider Toolkit (2009) ** http://code.google.com/p/gbif-providertoolkit 4

5. Data Harvest Infrastructure GIGA Registry (UDDI) New GIGA registry for germplasm dataset? ICIS and CropForge tools http://cropwiki.irri.org/icis/ https://cropforge.org/ GBIF data portal and registry** http://data.gbif.org gbrds.gbif.org (registry) GBIF Indexing Toolkit (2009) http://code.google.com/p/gbif-indexingtoolkit/ 5

6. Data Provider Software 6

7. EURISCO tab delimited upload http://eurisco.ecpgr.org 7

8. 8 BioMOBY The BioMOBY project was initiated in 2001 (in Saskatchewan, Canada). Two branches, web service and semantic (MOBY-S). MOBY ontology-aware registry for discovery of both data and services. Works well with TAPIR and BioCASE. GCP have selected BioMOBY as the main web service technology. http://biomoby.org

9. BioCASE 2.5 9 The BioCASE provider software is a product of the EU funded BioCASE project (2001-2004). Developed at BGBM in Berlin. Last updated in April 2008, with support for Python version 2.5 Data formats include: ABCD 2.06, Darwin Core, GCP_Passport, MCPD. http://www.biocase.org

11. Database connection

12. Database table structure

13. Mapping of data model to standard schema10

14. TAPIR TAPIR - TDWG Access Protocol for Information Retrieval. During the 2004 TDWG meeting in Christchurch, NZ, work started on a unified protocol and named TAPIR. TAPIR is based on the protocol from the two data provider software, BioCASE and DiGIR. 11

15. PyWrapper3 Home:http://trac.pywrapper.org/ Primary developers: Markus Döring, Javier de la Torre Source code: Python 14/07/2008 - Development stalled We are sorry to inform you that development of the TAPIR branch of PyWrapper has been stalled. The latest 3.1 alpha version is not stable and not recommended for production! (Message from the home page) PyWrapper is tested and verified to work fine with Windows, Mac OS X and Linux. 12

16. Web configuration tool PyWrapper graphical web based configuration tool 13

17. TapirLink 0.6.1 Home: http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink Primary developers: Renato De Giovanni, Dave Vieglais Download: http://sourceforge.net/project/showfiles.php?group_id=38190 Source code: PHP 14 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!

18. GBIF IPT Home: http://code.google.com/p/gbif-providertoolkit/ Primary developers: Markus Döring, Tim Robertson Download: http://code.google.com/p/gbif-providertoolkit/downloads/list Source code: Java 15 DEMO at http://atlas.nordgen.org/ipt/

20. The data registered in the IPT is connected to the GBIF distributed network and made available for public consultation and use.

21. Designed to transfer big amounts of records. Decentralize and speed up the process of indexing biodiversity occurrence datasets.

22. IPT also provides a local tool for data quality assessment to data publishers.

23. The data publisher will easily monitor data access and use.16

24. GBIF IPT 17

25. GBIF IPT 18

26. IPT 19

27. GBIF IPT 20

28. Web service interface 21

29. Example TAPIR service SEARCH request 22

30. Example TAPIR service Search response 23

31. Example of OAI-PMH service request Request types: Identify ListMetadataFormats ListSets GetRecord ListIdentifiers ListRecords http://an.oa.org/OAI-script?verb=GetRecord &identifier=oai:arXiv.org:hep-th/9901001 &metadataPrefix=oai_dc 24 OAI-PMH requests are submitted using either the HTTP GET or POST methods.

32. Example of OAI-PMH service RESPONSE 25 OAI-PMH responses formatted as HTTP. With The Content-Type as text/xml.

33. GBIF PGR Network 2 [http://data.gbif.org/datasets/network/2] 26

34. 27 Darwin Core A new version of Darwin Core is up for public review. http://rs.tdwg.org/dwc/terms/index.htm TDWG 2009, Montpellier, November 9 -13 DRAFT Germplasm extension http://code.google.com/p/darwincore/source/browse/#svn/trunk/xsd/profiles/germplasm RDF, LSID, ontology friendly

35. 28 Outlook The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community (GBIF, TDWG). Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work. Use of GBIF technology and integration of PGR collection data into GBIF allows PGR users to simultaneously search PGR collections and other biodiversity collections, and to get access to the data (and possibly the material) of relevant biodiversity collections. The establishment of new data portals and tools on a specific crop, a regional thematic network or similar subset of the total global biodiversity datasets; can be done with rather few efforts! Adopted from a slide by Helmut Knüpffer (IPK Gatersleben)

38. 31 http://wwwdev.ngb.se/portal/index.php?scope=demo

39. 32

40. 33

41. 34

42. 35

43. Data Harvest 36

44. GBIF GBRDS http://gbrds.gbif.org 37

45. GBIF GBRDS http://gbrds.gbif.org 38

46. Fallacies of Distributed Computing The network is reliable. Latency is zero. Bandwidth is infinite. The network is secure. Topology doesn't change. There is one administrator. Transport cost is zero. The network is homogeneous. This list of fallacies came about at Sun Microsystems around 1994. 39