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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.
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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
Genebanks as GBIF providers EURISCO and GBIF Web services The GBIF network model Possible EURISCO network
model
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
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
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
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)
Working Database
Online Database
Provider
Portal
Working Database
Working Database
The Data Provider is the web service package (wrapper) installed at the data source
The Data Portal is a gateway to data published from the data provider nodes
Provider
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
How does the GBIF model look like?
I have borrowed three slides from a presentation of the GBIF secretariat on this topic
Biodiversity Data Index
Services Registry
Nodes
Services
Records
GBIF Portal Participant Nodes Data Nodes
Taxonomic Name Service Specimen/Observation Service General Resource Service Name List Service …
Taxonomic Names Specimen/Observation Records HTML Pages Images …
holds metadata
for
provides index of
holds metadata
for
provide
supply
A simple DiGIR architecture (Slide borrowed from GBIF)
Data providers (have one or more databases to share and have installed DiGIR or BioCASe)
Databases
Portals, search engines, and applications developed for various purposes
Decentralised Centralised
Participant Portal A
Participant Portal C
Participant Portal B
Data Warehouse
GBIF Portal
GBIF Registry
GBIF Index
Data Warehouse
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?
Descriptors marked red did not match the earlier versions of ABCD ABCD was extended by a PGR section [W. Berendsohn, H. Knüpffer]
National Inventory Code Institute Code Accession Number Collecting Number Collecting Institute Code Genus Species Species Authority „Subtaxa“ „Subtaxa“ Authority Common Crop Name Accession Name Acquisition Date
Country of Origin Location of Collection
Site Latitude of CS Longitude of CS Elevation of CS Collecting Date of
Sample Breeding Institute Code Biological Status of
Accession Ancestral Data Collecting/Acquisition
Source
Donor Institute Code Donor Accession Number Other Identification (Number)
associated with the accession
Location of Safety Duplicates Type of Germplasm Storage Remarks Decoded Collecting Institute Decoded Breeding Institute Decoded Donor Institute Decoded Safety Duplication
Location Accession URL
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 parallell human network
Data Portal CCDB
Data Node
Genebank
Participant Node NI
Portal Node
EURISCO
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
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
Thank you for listening!