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Semantics for Biodiversity, May 16th – 18th 2012. Kansas University, Lawrence, KS. Dag Endresen, GBIF
genesys-pgr.orgThe GENESYS gateway to genetic resources provides access to information on morethan 2.3 million genebank ac...
Potential of the GBIF technologyhttp://data.gbif.org/datasets/network/2                                          3
Multiple data export services                                 European                                 Crop               ...
2005 : BioCASE demoGenebank/germplasm extension to the ABCD 2.06                                                5
2010 : IPT installations for EURISCO                      EURISCO                      NordGen (Nordic)                 ...
Darwin CoreThe purpose of DwC terms is to facilitate data sharing• a well-defined standard core vocabulary• a flexible fra...
Darwin Core extension for genebanksDwC Germplasm : DRAFT 0.1 : August 26, 2009• “MCPD in Darwin Core”• Additional terms to...
Alercia, A., S. Diulgheroff, T. Metz(2001). FAO/IPGRI Multi-croppassport descriptors, December2001. International Plant Ge...
DwC Germplasm (1)
DwC Germplasm (2)
DwC Germplasm (3)
DwC Germplasm (4)
DwC Germplasm (5)
Germplasm vocabulary of terms (RDF/SKOS)……    http://rs.gbif.org/sandbox/terms/germplasm/germplasm_01.rdf    http://purl.o...
Darwin Core Archive (DwC-A)   DwC-A publish dwc records including extensions   Simple text based format   Zipped single...
Darwin Core Archive extension (XML) …     http://rs.gbif.org/extension/nordgen/0.1/germplasm.xml                          ...
GBIF Vocabulary Serverhttp://vocabularies.gbif.org/node/163947                                    18
1. Mint and maintain concepts and terms,                                        in domain-expert working groups.          ...
Evaluation of various tools for collaborativemanagement of RDF vocabularies.                                              ...
http://community.gbif.org/pg/groups/21382/
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Darwin Core extension for genebanks (germplasm), at Kansas University (May 2012)

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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 (germplasm), at Kansas University (May 2012)

  1. 1. Semantics for Biodiversity, May 16th – 18th 2012. Kansas University, Lawrence, KS. Dag Endresen, GBIF
  2. 2. genesys-pgr.orgThe GENESYS gateway to genetic resources provides access to information on morethan 2.3 million genebank accessions, http://www.genesys-pgr.org/
  3. 3. Potential of the GBIF technologyhttp://data.gbif.org/datasets/network/2 3
  4. 4. Multiple data export services European Crop Databases European Genebank EURISCO dataset Catalog Global Crop GBIF Registries 4
  5. 5. 2005 : BioCASE demoGenebank/germplasm extension to the ABCD 2.06 5
  6. 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. 7. 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 natureas documented by observations, specimens, and samples, and relatedinformation.”http://rs.tdwg.org/dwc/The Darwin Core can be extended by new terms toshare 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. 8. Darwin Core extension for genebanksDwC 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 regulationshttp://code.google.com/p/darwincore-germplasmhttp://rs.nordgen.org/dwc/ (draft version)http://purl.org/germplasm/terms# (coming soon) 8
  9. 9. Alercia, A., S. Diulgheroff, T. Metz(2001). FAO/IPGRI Multi-croppassport descriptors, December2001. International Plant GeneticResources Institute (IPGRI) / Foodand Agriculture Organization of theUnited Nations (FAO), Rome, Italy.Available athttp://apps3.fao.org/wiews/mcpd/MCPD_Dec2001_EN.pdf 9
  10. 10. DwC Germplasm (1)
  11. 11. DwC Germplasm (2)
  12. 12. DwC Germplasm (3)
  13. 13. DwC Germplasm (4)
  14. 14. DwC Germplasm (5)
  15. 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. 16. Darwin Core Archive (DwC-A) DwC-A publish dwc records including extensions Simple text based format Zipped single file archive Germplasm.txt
  17. 17. Darwin Core Archive extension (XML) … http://rs.gbif.org/extension/nordgen/0.1/germplasm.xml 17
  18. 18. GBIF Vocabulary Serverhttp://vocabularies.gbif.org/node/163947 18
  19. 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. 20. Evaluation of various tools for collaborativemanagement 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. 21. http://community.gbif.org/pg/groups/21382/

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