Potential relationship and collaboration between EURISCO and GBIF - a distributed network of databases for the ECP/GR D&I network meeting at ZADI Bonn Germany 11th April 2005. Dag Endresen (Nordic Gene Bank). GBIF is a Global Biodiversity Information Facility for free and open access to biodiversity data.

1. Relationship
EURISCO and GBIF
a distributed network of databases
for the
ECP/GR D&I Network meeting
April 11, 2005 – ZADI, Bonn
Dag Terje Filip Endresen – The Nordic Gene Bank

2.  Genebanks as GBIF providers
 EURISCO and GBIF
 Web services
 The GBIF network model
 Possible EURISCO network
model

3.  IPK Gatersleben, Germany
109 711 records (BioCASE) August 2004
 National Centre for Plant Genetic
Resources, IHAR, Poland
40 459 records (DiGIR) March 2004
 The Nordic Gene Bank, NGB
26 868 records (DiGIR) March 2004

4. I will try to show that:
 The objective and mode of
operation of EURISCO and GBIF
overlaps
 The EURISCO network of National
Inventories (NIs) is similar to the
GBIF network of national Nodes
 The EURISCO network infrastructure
can be built based on GBIF and
TDWG standards and protocols

5.  ENBI is the EU's 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.
 The ENBI network is coordinated by the Zoological
Museum of the University of Amsterdam.
 BioCASE is represented in the membership of ENBI
 EPGRIS and EURISCO are represented in ENBI
 IPGRI is a member of ENBI (wp6)
http://www.enbi.info

6.  A Web service is a software system
identified by a URI, whose public
interfaces and bindings are defined
and described using XML. Its
definition can be discovered by other
software systems. These systems
may then interact with the Web
service in a manner prescribed by its
definition, using XML based messages
conveyed by Internet protocols.
(W3C, Web Services Glossary)

7.  The Data Provider is
Working Working Working
the web service Database Database Database
package (wrapper)
installed at the data Online
source
Database
Provider Provider
 The Data Portal is a
gateway to data
published from the
data provider nodes Portal

8.  A UDDI registry
manages information
about service providers,
service
implementations, and
service metadata.
 Service providers can
use the UDDI to
advertise the services
they offer.
 Service consumers
can use UDDI to
discover services to
obtain the service
metadata needed to
consume those services. You don’t get very far with web services
unless you have a registry...”
-Tom Gaskins, uddi.org

9. How does the GBIF model
look like?
I have borrowed three
slides from a presentation
of the GBIF secretariat on
this topic

10. holds Nodes GBIF Portal
metadata Participant Nodes
for Data Nodes
Services provide
Registry
holds Taxonomic Name Service
metadata Services Specimen/Observation Service
for General Resource Service
Name List Service …
supply
provides Taxonomic Names
index of Records Specimen/Observation Records
Biodiversity
Data Index HTML Pages
Images …

11. A simple DiGIR architecture
(Slide borrowed from GBIF)
Portals, search engines,
and applications
developed for various
purposes
Data providers
(have one or more
databases to share
and have installed
DiGIR or BioCASe)
Databases

12. GBIF GBIF GBIF
Registry Index Portal
Participant Participant Participant
Portal A Portal B Portal C
Data Data
Warehouse Warehouse
Decentralised Centralised

13. We need:
 Data provider software
can we use TAPIR, BioCASE or DiGIR?
 Data portal software
can we adopt the GBIF data portal software?
(can we also use the GBIF UDDI registry?)
 Network of people
we have the network of NIs from EPGRIS
we have the ECP/GR and the ECCDBs
 Standards and concepts
can we use ABCD, (Darwin Core 2)?
is ABCD sufficiently compatible with MCPD?

14. National Inventory Code Country of Origin Donor Institute Code
Institute Code Location of Collection Donor Accession Number
Site Other Identification (Number)
Accession Number
Latitude of CS associated with the
Collecting Number accession
Longitude of CS
Collecting Institute Code Location of Safety Duplicates
Elevation of CS
Genus Collecting Date of Type of Germplasm Storage
Species Sample Remarks
Species Authority Breeding Institute Code Decoded Collecting Institute
„Subtaxa“ Biological Status of Decoded Breeding Institute
Accession Decoded Donor Institute
„Subtaxa“ Authority
Ancestral Data Decoded Safety Duplication
Common Crop Name
Collecting/Acquisition Location
Accession Name Source Accession URL
Acquisition Date
 Descriptors marked red did not match the earlier versions of ABCD
  ABCD was extended by a PGR section [W. Berendsohn, H. Knüpffer]

15.  The accession (passport)
data is curated and Data
Portal
shared from the local CCDB
genebank node
 Data to EURISCO is
endorsed by the NI Portal
Node
 The EURISCO data EURISCO
portal node provides
access to the data for the
ECCDBs
Data Participant
There is no data network Node Node
without a parallell human Genebank NI
network

16.  The new unified protocol TAPIR
(Python wrapper under development) may
be a good choice
 Implement BioCASE (while TAPIR
develops), ABCD includes MCPD in
the PGR unit
 DiGIR implements Darwin Core,
where mapping to MCPD is
uncomplete

17.  Develop new PGR portal
software (based on SOAP)
(under development?)
 Adopt the GBIF portal
software (based on Java and MySQL,
free open source, but installation
package not completed yet)
 Develop a specific EURISCO
UDDI registry or explore
alternative to use the GBIF
UDDI registry

18. Thank you for listening!