The Darwin Core terms can be seen as an extension to the standard Dublin Core metadata terms. The new Darwin Core extension for genebanks declares the additional terms required for describing genebank datasets, and is based on established standards from the plant genetic resources community. The Global Biodiversity Information Facility (GBIF) provides an information infrastructure for biodiversity data including a suite of software tools for data publishing, distributed data access, and the capture of biodiversity data. The Darwin Core extension for genebanks is a key component that provides access for the genebanks and the plant genetic resources community to the GBIF informatics infrastructure including the new toolkits for data exchange.

1. Semantics for Biodiversity, May 16th – 18th 2012. Kansas University, Lawrence, KS. Dag Endresen, GBIF

2. genesys-pgr.org
The GENESYS gateway to genetic resources provides access to information on more
than 2.3 million genebank accessions, http://www.genesys-pgr.org/

3. Potential of the GBIF technology
http://data.gbif.org/datasets/network/2
3

4. Multiple data export services
European
Crop
Databases
European
Genebank EURISCO
dataset Catalog
Global Crop
GBIF Registries
4

5. 2005 : BioCASE demo
Genebank/germplasm extension to the ABCD 2.06
5

6. 2010 : IPT installations for EURISCO
 EURISCO
 NordGen (Nordic)
 Bioversity-Montpellier (France)
 IPK Gatersleben (Germany)
 BLE (Germany)
 WUR CGN (The Netherlands)
 CRI (Czech Republic)
 VIR (Russian Federation)
 SeedNET (Balkan)
 Baltic (Estonia, Latvia, Lithuania)
6

7. Darwin Core
The purpose of DwC terms is to facilitate data sharing
• a well-defined standard core vocabulary
• a flexible framework to maximize re-usability
• approved as TDWG standard 2009
“The Darwin Core is primarily based on taxa, their occurrence in nature
as documented by observations, specimens, and samples, and related
information.”
http://rs.tdwg.org/dwc/
The Darwin Core can be extended by new terms to
share additional information.
Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, Giovanni R,
Robertson T, Vieglais D (2012). Darwin Core: An Evolving Community-
Developed Biodiversity Data Standard. PLoS ONE 7(1): e29715.
doi:10.1371/journal.pone.0029715
7

8. Darwin Core extension for genebanks
DwC Germplasm : DRAFT 0.1 : August 26, 2009
• “MCPD in Darwin Core”
• Additional terms to describe germplasm samples
• Includes terms from the breeding/cultivation event
• Includes additional terms for crop trait experiments
• Includes terms for international crop treaty regulations
http://code.google.com/p/darwincore-germplasm
http://rs.nordgen.org/dwc/ (draft version)
http://purl.org/germplasm/terms# (coming soon)
8

9. Alercia, A., S. Diulgheroff, T. Metz
(2001). FAO/IPGRI Multi-crop
passport descriptors, December
2001. International Plant Genetic
Resources Institute (IPGRI) / Food
and Agriculture Organization of the
United Nations (FAO), Rome, Italy.
Available at
http://apps3.fao.org/wiews/mcpd/MCPD_
Dec2001_EN.pdf
9

10. DwC Germplasm (1)

11. DwC Germplasm (2)

12. DwC Germplasm (3)

13. DwC Germplasm (4)

14. DwC Germplasm (5)

15. Germplasm vocabulary of terms (RDF/SKOS)
…
…
http://rs.gbif.org/sandbox/terms/germplasm/germplasm_01.rdf
http://purl.org/germplasm/ (in preparation)
http://kos.gbif.org/wiki/Germplasm (wiki forum) 15

16. Darwin Core Archive (DwC-A)
 DwC-A publish dwc records including extensions
 Simple text based format
 Zipped single file archive
Germplasm.txt

17. Darwin Core Archive extension (XML)
…
http://rs.gbif.org/extension/nordgen/0.1/germplasm.xml
17

18. GBIF Vocabulary Server
http://vocabularies.gbif.org/node/163947
18

19. 1. Mint and maintain concepts and terms,
in domain-expert working groups.
2. Release final version as a RDF Vocabulary.
3. REUSE terms from published RDF vocabularies
Wiki and ontologies when designing new DwC-A
Vocabulary extensions, controlled value vocabularies
Management (and new Ontologies). 4
1 4. Publish at the GBIF Resources Repository.
5. Browse at the GBIF Resources Browser.
Resources
Repository
RDF 2
Vocabulary
ISOcat GBIF 5
Vocabulary of Concepts Resources
Management (rdf, skos) Browser
1
proposed
spreadsheet
processor Darwin Core
Archive
extensions &
Excel controlled GBIF Vocabularies
3 vocabularies as a collaborative
Template for management tool for
Vocabularies Darwin Core Archive
1 GBIF Vocabularies extensions and controlled
vocabularies.
Collaborative management tools

20. Evaluation of various tools for collaborative
management of RDF vocabularies.
GBIF
Resources
Repository
Wiki
Vocabulary
Management Resources
RDF Repository
Vocabulary DwC-A
ISOcat
of Concepts Extensions & GBIF IPT
Controlled
Vocabulary
Management (rdf, skos) vocabularies
?
proposed Scratchpads
spreadsheet
processor
MS Excel
Template for
Vocabularies Wiki Forum Wiki forum for terms as
for Terms an open community
platform for description
of new and (reused)
existing terms.

21. http://community.gbif.org/pg/groups/21382/