ALIS’s Adventures in Wonderland

Samy Gaiji, SINGER CoordinatorSonia Dias, EURISCO Coordinator

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 areasThe 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

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…)

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.

Understanding Diversity

Genebanks

Maize

Potato

Rice

Understanding Genebanks

Genebanks

Breeding

Evaluation

Distribution

Characterization

Scientific Standards

Like DarwinCore

Common to all crops

Crop specific>80 crops

Scientific Standards

Common to all crops

Holding/GenebankHolding/CollectionTax/GenusTax/SpeciesTax/SubSpeciesOrigin/CountryOrigin/LatitudeOrigin/LongitudeMission/Collector(s)Mission/CountryMission/Location…/…

Pas s

por t

data

Crop specific

1:1

Plant/LeafPlant/LeafFormPlant/…Inflorescence/FlowercolorInflorescence/DateofInflorescence/TypeFruit/ColorFruit/StructureFruit/…Molecular/SNP-XYZMolecular/SNP-ABC…/…

1:∞

DateLocationYield (kg/ha)

Scientific Standards

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.

Existing information sharinginfrastructure

GenebankInformationsystems

NetworkPortal

GlobalPortal

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)

69%13%

5%13%

Landrace

Wild

Breeding

Others

EURISCO for the Europe

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

What we did in 2006-2007

ABCD

‘ALIS’

Global accession level information system

‘ALIS’

What we did in 2006-2007

ALIS

(ex-C

HM

)

What we did in 2006-2007

Plant Genetic Resources Unit in ABCD

What we did in 2006-2007

Exam

ple

of

resp

on

se f

or

‘ALIS

’

What we did in 2006-2007

(Now migrating to TAPIR/pywrapper)

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

BIOCASE Infrastructure (>20 providers)

What we did in 2006-2007

≈33%

What we did in 2006-2007

What we did in 2006-2007

What we did in 2006-2007

Bioinformatics Domain Model Platform (GCP)

Domain Model Layer

LocalDatabase

Web ServiceProvider

Inte

rnet

UserTools &

InterfacesViews

Middleware

Data Sources

Data Access Interface

View/Query Interface

Web ServiceData Source

Java BeansSQL

XML

XML

JSPJava Beans

What we did in 2006-2007

Bioinformatics Domain Model to Platform (GCP)

Inte

rnet

Domain Model Layer

LocalDatabase

Middleware

Data Sources

Web services ‘depot’

: Moby Web Services

CNS: Concept Name Server

What we did in 2006-2007

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.

The new Wonderland…

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

The new Wonderland…

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

The new Wonderland…

Treaty

Global Information System

Benefit Sharing Mechanism

Funding Mechanism

The new Wonderland…

Global Information System

Global Accession Level Information System

‘ALIS’= “Who has What and Where?”

pywrapper pywrapper pywrapper pywrapper pywrapper pywrapper pywrapper

The Wonderland…

Global Information System

CNS: Concept Name Server

© Markus DoeringABCD 2.06

ALIS 1.0

The new Wonderland…

Persistent Identifiers of providers and recipientsof germplasm.

Accession level Information System

(passport, characteristics,performances …

of germplasm)Germplasm OrderingTool Kit handling therequests of germplasm and issuing legal agreement between providers and recipients.

TAPIR/pywrapper

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.

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).

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

"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