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

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Presentation on theme: "ALIS’s Adventures in Wonderland Samy Gaiji, SINGER Coordinator Sonia Dias, EURISCO Coordinator."— Presentation transcript:

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

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 Genebanks Maize Potato Rice

6 Understanding Genebanks Genebanks Breeding Evaluation Distribution Characterization

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

8 Scientific Standards Common to all crops Holding/Genebank Holding/Collection Tax/Genus Tax/Species Tax/SubSpecies Origin/Country Origin/Latitude Origin/Longitude Mission/Collector(s) Mission/Country Mission/Location …/… Passport data Crop specific 1:1 Plant/Leaf Plant/LeafForm Plant/… Inflorescence/Flowercolor Inflorescence/Dateof Inflorescence/Type Fruit/Color Fruit/Structure Fruit/… Molecular/SNP-XYZ Molecular/SNP-ABC …/… 1:∞ Date Location Yield (kg/ha)

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 Existing information sharing infrastructure Genebank Information systems Network Portal Global Portal

12 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 ( 69% 13% 5% 13% Landrace Wild Breeding Others

13 EURISCO for the Europe >1,000,000 accessions, 35 countries >200 holding institutions (genebanks) etc… (

14 What we did in 2006-2007 ABCD ‘ALIS’ Global accession level information system ‘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 (Now migrating to TAPIR/pywrapper) BIOCASE Infrastructure (>20 providers)

19 What we did in 2006-2007 ≈33%

20 What we did in 2006-2007


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

23 What we did in 2006-2007 Bioinformatics Domain Model to Platform (GCP) Internet Domain Model Layer Local Database Middleware Data Sources Web services ‘depot’ : 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 The new Wonderland… In 2006, the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) entered into force.

27 The new Wonderland…

28 More than 110 contracting parties !!!!

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

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

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

32 The new Wonderland… Persistent Identifiers of providers and recipients of germplasm. Accession level Information System (passport, characteristics, performances … of germplasm) Germplasm Ordering Tool Kit handling the requests of germplasm and issuing legal agreement between providers and recipients. 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

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