Post on 14-Dec-2015
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