EURISCO needs and priorities, at CGIAR ICT-KM Workshop, IPGRI, Rome (2005)

The Nordic Gene Bank, NGB, Alnarp, SwedenThe Nordic Gene Bank, NGB, Alnarp, Sweden

European Gene Banks, EURISCO and NGB

Overview of Needs and Priorities

Training Workshop on interoperability

June 14, 2005 – IPGRI, Rome

Dag Terje Filip Endresen – The Nordic Gene Bank

2GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome

TOPICS for this presentationTOPICS for this presentation

European Gene Banks (ECP/GR)

European Central crop databases

EURISCO Nordic Gene banks Conclusions


EURISCO and GBIFEURISCO and GBIF

I will try to show that: The objective and mode of operation of

EURISCO, (SINGER) and GBIF overlaps.

The EURISCO network of National Inventories (NIs) is similar to the SINGER network of CGIAR Centers and to the GBIF network of national Nodes.

The EURISCO (and SINGER) network infrastructure can be built based on GBIF and TDWG standards and protocols.


EEuropean uropean CCooperative ooperative PProgramme rogramme for Crop for Crop GGenetic enetic RResources Networksesources Networks

More than 50 „Central Crop Databases“ in Europe > 20 years (Wheat, Potato, Barley etc.)

EURISCO – central inventory of plant genetic resources in Europe.

- EU project EPGRIS (1999-2003)- 42 national programs (Europe)- at present 920,147 accessions

approximately 50% of the estimated accessions in European genebanks.

ECP/GRECP/GR


European PGR Network modelEuropean PGR Network model

The accession (passport) data is curated and shared from the local genebank node

Data to EURISCO is endorsed by the NI

The EURISCO data portal node provides access to the data for the ECCDBs

There is no data network without a parallel human network.

DataPortal

ECCDB

Data Node

Gene bank

ParticipantNode

NI

PortalNode

EURISCO

Data flow


PGR Data Flow in Europe PGR Data Flow in Europe Frank Begemann, Frank Begemann, ECP/GRECP/GR

*At the discretion of the National Focal Point ** Data flow for char. & evaluation data to be discussed


Where we are today Where we are today (Europe)...(Europe)...

Dataflow from gene bank to EURISCO and ECCDB as flat files, tab-separated MCPD.

MCPD

eMCPD

NationalInventor

y

EURISCOCentralData

warehouse

MCPD+cropspecificdescripto

rs

Central Crop

DatabaseECCDB

Gene Bank

Databases Central

Data warehouse model


Future decentralized model...Future decentralized model...

Dataflow from gene bank to EURISCO and ECCDB through decentralized web services.

XML

Gene BankDatabase

[1]

Web Service layer (agreed standards and data provider software)

Central

CropPortal

EURISCO

Portal

GBIFPortal etc..

.XM

LXM

LXM

L

National Inventor

yPortal

XML

BioCASEPortal

XML

XML

Gene BankDatabase

[2]

etc...


Real world, mixed model...Real world, mixed model...Dataflow from gene bank to EURISCO and ECCDB through decentralized web services.

NationalInventory

EURISCO

database

XML

Central Crop

DatabaseECCDB

Gene BankDatabase

Web Service layer (agreed standards and data provider software)

XML

XML

XML

ECCDBPortal

EURISCO

Portal

GBIFPortal

etc...XM

LXM

LXM

L

NIPortal

XML

BioCASE

PortalXM

L

Gene Bank

Database

Gene Bank

DatabaseOther

DatabaseGene Bank

Database

OtherDatabaseOther

Datasource

Gene Bank

DatabaseOther

Datasource


Nordic and Baltic PGR Nordic and Baltic PGR collaborationcollaboration

NGB is coordinating the international regional network of Nordic and Baltic genebanks.


Nordic Baltic Regional PGR Nordic Baltic Regional PGR networknetwork

SESTO is the common regional documentation platform for data management.

Improved data exchange models and network infrastructure is needed to develop this model further.


EURISCO as a network of web servicesEURISCO as a network of web services

EURISCO (& NGB) needs: Data provider software

can we use BioCASE or DiGIR (BioMOBY??)

Data portal softwarecan we adopt the GBIF or BioCASE data portal software?can we use the GBIF UDDI registry?

Network of peoplewe have the network of NIs from EPGRISwe have the ECP/GR and the ECCDBs

Data standardscan we use ABCD, (Darwin Core 2)?ABCD 2.0 is compatible with MCPD


Choosing the data provider Choosing the data provider softwaresoftware

The new unified protocol specification TAPIR (implementation for BioCASE and DiGIR?)

Implement BioCASE, ABCD is compatible with MCPD and has a separate PGR sub-unit.

DiGIR use Darwin Core, where mapping to MCPD is incomplete (?)


Choosing the data portal softwareChoosing the data portal software

Develop a specific EURISCO UDDI registry or explore alternatives to use the GBIF UDDI registry

Adopt the GBIF portal software for EURISCO (based on Java and MySQL, free open source)

Adopt the BioCASE portal software (based on Python, free open source)


European Genebanks as GBIF European Genebanks as GBIF providersproviders

IPK Gatersleben, Germany109 711 records (BioCASE) August 2004

National Centre for Plant Genetic Resources, IHAR, Poland40 459 records (DiGIR) March 2004

The Nordic Gene Bank, NGB26 868 records (BioCASE, DiGIR) March 2004

EURISCO (2005 ...??)


ENBIENBI EEuropean uropean NNetwork for etwork for BBiodiversity iodiversity IInformationnformation

ENBI is an European contribution to the Global Biodiversity Information Facility (GBIF).

ENBI is a thematic network supported by the European Commission under the fifth Framework Programme and contributing to the "Energy, environment and sustainable development" programme. Contract no EVK2-CT-2002-20020.

EPGRIS and EURISCO are represented in ENBI IPGRI is a member of ENBI (wp6)

BioCASE is represented in the membership of ENBI

[http://www.enbi.info]


EPGRIS-2EPGRIS-2

EPGRIS-2 project under development, expected to start in 2006.

WP1 Coordination WP2 Data standards WP3 Network infrastructure WP4 Capacity development WP5 Pilot Crop portals WP6 GIS visualization WP7 Taxonomy


Major Global Crop collectionsMajor Global Crop collections

EURISCO is an inventory of 926,231 accessions from European Gene Banks

The CGIAR Gene Banks hold over 530,000 samples of wild and domesticated crops in public trust.

USDA-Grin holds 464,389 accessions.

Accessions in EURISCO (926,231)Accessions in EURISCO (926,231)

Accessions in SINGER Accessions in SINGER (524,466)(524,466)


ConclusionsConclusions

To build the genetic resources infrastructure on GBIF technology and global biodiversity standards.

All European Gene banks to join GBIF through EURISCO.

Will the CGIAR Future Harvest Centers join GBIF through SINGER?

Will USDA-GRIN join GBIF? Will BioMOBY join GBIF??


Thank you for listening!

Technology

EURISCO needs and priorities, at CGIAR ICT-KM Workshop, IPGRI, Rome (2005)