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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.
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Darwin Core extension for genebanks
Semantics for Biodiversity, May 16th – 18th 2012. Kansas University, Lawrence, KS. Dag Endresen, GBIF
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/
Potential of the GBIF technology
http://data.gbif.org/datasets/network/2 3
Genebankdataset
Global Crop Registries
European EURISCO Catalog
European Crop Databases
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GBIF
Multiple data export services
2005 : BioCASE demo
Genebank/germplasm extension to the ABCD 2.065
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)
2010 : IPT installations for EURISCO
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Darwin CoreThe 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
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http://code.google.com/p/darwincore-germplasm
http://rs.nordgen.org/dwc/ (draft version)
http://purl.org/germplasm/terms# (coming soon)
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
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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
DwC Germplasm (1)
DwC Germplasm (2)
DwC Germplasm (3)
DwC Germplasm (4)
DwC Germplasm (5)
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Germplasm vocabulary of terms (RDF/SKOS)…
…http://rs.gbif.org/sandbox/terms/germplasm/germplasm_01.rdfhttp://purl.org/germplasm/ (in preparation)http://kos.gbif.org/wiki/Germplasm (wiki forum)
Darwin Core Archive (DwC-A) DwC-A publish dwc records including
extensions Simple text based format Zipped single file archive
Germplasm.txt
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Darwin Core Archive extension (XML)
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http://rs.gbif.org/extension/nordgen/0.1/germplasm.xml
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GBIF Vocabulary Server
http://vocabularies.gbif.org/node/163947
RDF Vocabulary of Concepts(rdf, skos)
Wiki VocabularyManagement
ISOcat VocabularyManagement
Excel Template forVocabularies
GBIFResources Browser
Resources Repository
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 and ontologies when designing new DwC-A extensions, controlled value vocabularies (and new Ontologies).4. Publish at the GBIF Resources Repository.5. Browse at the GBIF Resources Browser.
GBIF Vocabularies
Darwin Core Archiveextensions &controlled vocabularies
Collaborative management tools
proposed spreadsheet processor
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GBIF Vocabularies as a collaborative management tool for Darwin Core Archive extensions and controlled vocabularies.
RDF Vocabulary of Concepts(rdf, skos)
Wiki VocabularyManagement
ISOcat VocabularyManagement
MS Excel Template forVocabularies
Resources Repository
Evaluation of various tools for collaborative management of RDF vocabularies.
DwC-AExtensions &Controlled vocabularies
GBIFResources
Repository
GBIF IPT
Scratchpads
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proposed spreadsheet processor
Wiki Forum for Terms
Wiki forum for terms as an open community platform for description of new and (reused) existing terms.
http://community.gbif.org/pg/groups/21382/
