ALIS’s Adventures in Wonderland

1. ALIS’s Adventures in Wonderland Samy Gaiji, SINGER Coordinator Sonia Dias, EURISCO Coordinator

2. Bioversity is the world's largest international research organization dedicated solely to the conservation and use of agricultural biodiversity. It is non-profit and independently operated. Our focus areas The purpose of Bioversity ’s work is to ensure that individuals and institutions are able to make optimal use of agricultural biodiversity to meet current and future development needs of people and societies. To achieve this purpose, Bioversity concentrates on six focus areas: * developing and implementing strategies for global collaboration to conserve and use genetic resources for food and agriculture that focus on policies, genetic resources information systems and awareness raising; * monitoring the status and trends of useful diversity, including locating diversity in situ and genetic erosion; * enhancing the ex situ conservation and use of diversity of useful species; * conservation and sustainable use of important wild species; * managing agricultural biodiversity for better nutrition, improved livelihoods and sustainable production systems for the poor; and * conserving and promoting the use of diversity of selected high value crops for the poor http://www.bioversityinternational.org

3. Purpose of this presentation: • Present the strategies for the: • data integration within the genebank community. • data integration with other communities (e.g. bioinformatics). • integration of BIOCASE and now TAPIR protocols within existing community ‘middleware’. • integration of information sharing infrastructure and data within a broader framework (Policy, Benefit Sharing, Research…)

4. Some History… Nikolai Ivanovich Vavilov(1887-1943) Prominent Russian botanist and geneticist best known for having identified the centres of origin of cultivated plants. He devoted his life to the study and improvement of wheat, corn, and other cereal crops that sustain the global population.

5. Understanding Diversity Rice Genebanks Potato Maize

6. Understanding Genebanks Characterization Genebanks Evaluation Breeding Distribution

7. Scientific Standards Crop specific >80 crops Common to all crops Like DarwinCore

8. Scientific Standards Common to all crops Crop specific Holding/GenebankHolding/CollectionTax/GenusTax/SpeciesTax/SubSpeciesOrigin/CountryOrigin/LatitudeOrigin/LongitudeMission/Collector(s)Mission/CountryMission/Location…/… Plant/LeafPlant/LeafFormPlant/…Inflorescence/FlowercolorInflorescence/DateofInflorescence/TypeFruit/ColorFruit/StructureFruit/…Molecular/SNP-XYZMolecular/SNP-ABC…/… Passport data 1:1 DateLocationYield (kg/ha) 1:∞

9. Scientific Standards

10. Management Systems • A majority of genebanks have already in place ‘good’ management systems (e.g. Europe, North America, CGIAR, etc…). • Agreed international scientific standards (aka Bioversity descriptors) are well adopted and used in existing information systems. • Best practices for managing collections are ‘in general’ followed by existing genebank management systems.

11. Global Portal Existing information sharinginfrastructure Network Portal Genebank Information systems

12. Breeding Others 13% 5% Landrace 13% 69% Wild SINGER for the CGIAR • Members: 11 genebanks • Holdings: >700,000 accessions (12% of world holdings) • Diversity: very rich material (mostly landraces and wild relatives) • Information: well documented (passport, characterization, evaluation, distribution etc…) • Availability: as Global Public Good(http://singer.cgiar.org)

13. EURISCO for the Europe >1,000,000 accessions, 35 countries>200 holding institutions (genebanks) etc… (http://eurisco.ecpgr.org)

14. What we did in 2006-2007 Global accession level information system ‘ALIS’ ABCD ‘ALIS’

15. What we did in 2006-2007 ALIS (ex-CHM)

16. What we did in 2006-2007 Plant Genetic Resources Unit in ABCD

17. What we did in 2006-2007 Example of response for ‘ALIS’

18. What we did in 2006-2007 BIOCASE Infrastructure (>20 providers) (Now migrating to TAPIR/pywrapper)

19. What we did in 2006-2007 ≈33%

20. What we did in 2006-2007

21. What we did in 2006-2007

22. Java Beans SQL Web Service Data Source What we did in 2006-2007 Bioinformatics Domain Model Platform (GCP) Internet Web Service Provider User Tools & Interfaces Views XML JSP View/Query Interface Java Beans Domain Model Layer Middleware Data Access Interface Local Database Data Sources XML

23. What we did in 2006-2007 Bioinformatics Domain Model to Platform (GCP) Internet Middleware Domain Model Layer Web services ‘depot’ CNS Local Database Data Sources : Moby Web Services CNS: Concept Name Server

24. What we did in 2006-2007

25. Impact • Fast migration of existing standards into XML schema -> ALIS Master Schema <-> ABCD • Wide adoption of BIOCASE and now TAPIR protocols (Genebank community but now also molecular and breeding communities) • Fast deployment of BIOCASE and now TAPIR/pywrapper applications. • Increased interest in TDWG activities. • Increased membership to GBIF.

26. In 2006, the International Treaty on Plant Genetic Resourcesfor Food and Agriculture (ITPGRFA) entered into force. The new Wonderland…

27. The new Wonderland…

28. The new Wonderland… More than 110 contracting parties !!!!

29. The new Wonderland… Treaty Global Information System Benefit Sharing Mechanism Funding Mechanism

30. pywrapper pywrapper pywrapper pywrapper pywrapper pywrapper pywrapper The new Wonderland… Global Information System Global Accession Level Information System ‘ALIS’ = “Who has What and Where?” ALIS

31. © Markus Doering The Wonderland… Global Information System ALIS CNS ABCD 2.06 ALIS 1.0 CNS: Concept Name Server

32. The new Wonderland… Persistent Identifiersof providers and recipientsof germplasm. PID Accession level Information System(passport, characteristics,performances … of germplasm) ALIS Germplasm OrderingTool Kit handling therequests of germplasm and issuing legal agreement between providers and recipients. OTK TAPIR/pywrapper

33. 2008-2010 Targets • By 2010, 85% of global holdings are available through ALIS and GBIF Portals using TDWG standards/tools. • By 2010, 70% of the genebanks will be linked to the ALIS infrastructure (>500 providers). • By 2009, schema for 22 crops will be computerized into the ALIS master schema and linked to ABCD. • By 2010, a global germplasm ordering system linked to the benefit-sharing mechanism of the Treaty will be operational. • By 2010, the ALIS infrastructure will be financially sustained through a multi-donors trust fund.

34. Key issues for TDWG • Raise awareness within our institutions about TDWG. • Increase participation/memberships from the genebank community to sustain core TDWG activities. • Explore ways to include an overhead charge within our restricted projects to sustain targeted TDWG activities. • Ensure sustainability of TAPIR/pywrapper application and help-desk for the period 2008-2010 (full time developer? maintenance contract? small grants?). • Promote TDWG standards and tools within and outside our scientific communities (e.g. molecular… breeders…policy).

35. Acknowledgments • A particular thank to: • Helmut Knuepffer (IPK) • Donald Hobern (GBIF) • Markus Döring (BGBM) • Javier de la Torre (ex-BGBM) • Dag Terje Endresen Filip (NGB) • Walter Berendsohn (BGBM) • TDWG community

36. "Begin at the beginning," the King said, gravely, "and go on till you come to the end; then stop.” Lewis Carrol, Alice's Adventures in Wonderland