EURISCO and GBIF, at the European genbank network meeting (Bonn, April 2004)
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EURISCO and GBIF, at the European genbank network meeting (Bonn, April 2004)

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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......

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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  • 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!