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European genebanks, EURISCO and NGB. Overview of needs and priorities. CGIAR ICT-KM training workshop on information interoperability, 14th June 2005, IPGRI Rome Italy. Dag Endresen (Nordic Gene Bank).
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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
3GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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.
4GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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
5GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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
6GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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
7GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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
8GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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...
9GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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
10GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
Nordic and Baltic PGR Nordic and Baltic PGR collaborationcollaboration
NGB is coordinating the international regional network of Nordic and Baltic genebanks.
11GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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.
12GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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
13GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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 (?)
14GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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)
15GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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 ...??)
16GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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]
17GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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
18GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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)
19GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
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??
20GCP and SGRP workshop on interoperability June 13, 2005, IPGRI, RomeGCP and SGRP workshop on interoperability June 13, 2005, IPGRI, Rome
Thank you for listening!
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