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!