Web service demo for EURISCOGBIF Tools and Darwin Core extension for germplasm

N.I. Vavilov Research Institute of Plant Industry (VIR), April 26th – 29th 2010, St Petersburg, Russian FederationDag Endresen, Jonas Nordling, Nordic Genetic Resources Center (NordGen)

Topics for this session

Web service installations for EURISCO Overview of the current project Darwin Core and the extension for

germplasm GBIF informatics tools Integrated Publishing Toolkit (IPT) Distributed datasets

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Possible Upgraded PGR Network Model

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The gene bank dataset is shared from the holding gene bank.

The National Inventory (NI) endorse all national gene banks (and eventually individual accessions) for EURISCO.

ECPGR Crop databases can access passport data from EURISCO and additional crop specific data from the genebank IPT interface.

Standard data sharing tools ensure that the genebank dataset is available to other relevant decentralized thematic, regional or global networks.

Objectives of the EURISCO demo project

Evaluate the GBIF decentralized architecture

Install the IPT installation for 8 genebanks in Europe that, as far as possible, are also EURISCO/ECPGR partners.

Test the registration of IPT installation through the GBIF registryGlobal Biodiversity Resources Discovery System (GBRDS).

Test the Harvesting and Indexing Toolkit (HIT) installation for the EURISCO platform (Bioversity HQ, Rome).

Project runs until 20 December 2010.

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EURISCO NordGen (Nordic) Bioversity-Montpellier

(France) IPK Gatersleben (Germany) BLE (Germany) WUR CGN (The

Netherlands) CRI (Czech Republic) VIR (Russian Federation) SeedNET (Balkan) Baltic (Estonia, Latvia,

Lithuania)

2010 : IPT installations for EURISCO

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2005 : BioCASE demo

http://chm.grinfo.net/6

Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.

The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community (TDWG, GBIF).

Potential of the GBIF technology

http://data.gbif.org/datasets/network/2

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Darwin CoreThe purpose of DwC terms is to facilitate data sharing • a well-defined standard core vocabulary

• a flexible framework to maximize re-usability

The Darwin Core can be extended by adding new terms to share additional information.

Approved as TDWG standard 2009

“The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information.”

http://rs.tdwg.org/dwc/

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http://code.google.com/p/darwincore-germplasm

http://rs.nordgen.org/dwc

DwC extension for germplasm

DwC Germplasm : DRAFT 0.1 : August 26, 2009

• “MCPD in Darwin Core”

• Maintained by gene banks worldwide

• Additional terms to describe germplasm samples

• Includes the new terms for crop trait experiments developed as part of the European EPGRIS3 project

• Includes a few additional terms for new international crop treaty regulations

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Mapping of DwC-G terms to the MCPD descriptors

(EURISCO data exchange format)

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Mapping of DwC-G terms to the MCPD descriptors (continued)

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MCPD -> ABCD 2.06 (2004) for BioCASE

National Inventory CodeInstitute CodeAccession NumberCollecting NumberCollecting Institute CodeGenusSpeciesSpecies Authority„Subtaxa“„Subtaxa“ AuthorityCommon Crop NameAccession NameAcquisition Date

Country of OriginLocation of Collection SiteLatitude of CSLongitude of CSElevation of CSCollecting Date of SampleBreeding Institute CodeBiological Status of

AccessionAncestral DataCollecting/Acquisition

Source

Donor Institute CodeDonor Accession NumberOther Identification (Number)

associated with the accessionLocation of Safety DuplicatesType of Germplasm StorageRemarksDecoded Collecting InstituteDecoded Breeding InstituteDecoded Donor InstituteDecoded Safety Duplication

LocationAccession URL

Helmut KnüpfferIPK Gatersleben

Walter BerendsohnBGBM

http://www.ecpgr.cgiar.org/epgris/Tech_papers/EURISCO_Descriptors.pdf

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GBIF Informatics Suite

GBIF tools to empower decentralized thematic or regional networks

Darwin Core extension for germplasm makes these tools usable for crop gene banks.

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A tool for data publishers.

A simple mechanism to share primary biodiversity data following the Darwin Core standard.

Open source, Java based web application.

Provides a local tool for data quality assessment, etc.

Integrated Publishing Toolkit (IPT)

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• Embeds its own database

• Multilingual

• Has a user management feature based on roles, which allows for multiple data managers to share a common instance

• Manages multiple data sources

• Several upload options: relational database management systems or data files

• Public web interface allows for data browsing and full text search

• Customised detail pages

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The IPT user interface includes

the germplasm extension

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XML interface includes thegermplasm extension

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VIR (RUS001)Passport data

VIR (RUS001)Crop departments

Global Crop Registries

European EURISCO Catalog

European ECPGR Crop Databases

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VIR (RUS001)Passport data

VIR Crop dataset

Global Crop Registries

EURISCO

ECPGR Crop Databases

Same dataset available from multiple information systems...

?!

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VIR (RUS001)Passport data

VIR Crop dataset

Global Crop Registries

EURISCO

ECPGR Crop Databases

Resolvable persistent identifiers can direct the user to the publisher of the primary dataset (official original dataset)

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• The Persistent Identifier (PI) is a digital name tag– Also called Global Unique Identifiers (GUID)– Life Science Identifiers (LSID) is one example– Digital Object Identifier (doi) is another example

• The Persistent Identifier concept for to naming and identification of data resources stored in multiple, distributed data stores.

• Effective identification of data objects is essential for linking the world’s biodiversity data.

Persistent Identifier

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Global crop collections

Moving towards… global integration of information

Threatened species

Migratory species

Spatial data

Global crop system

Crop standards

Legislation and regulations etc.

Crop collections in Europe

Genebank datasets

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• GBIF, Global Biodiversity Information Facility http://www.gbif.org

• TDWG, Biodiversity Information Standards http://www.tdwg.org

• Bioversity International http://www.bioversityinternational.org

Things can happen in a band, or any type of collaboration, that would not otherwise happen. (Jim Coleman, Musician)

Special thanks to: