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 …

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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  • Endresen, D., S. Gaiji, T. Robertson (2009). DarwinCore Germplasm Extension and deployment in the GBIF infrastructure. Proceedings of TDWG 2009, Montpellier, France. Bioversity Information Standards (TDWG). Available at http://www.tdwg.org/proceedings/article/view/464, verified 21 Feb 2012. Endresen, D.T.F. and H. Knüpffer (2011). The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets. p. 119-142. In: Endresen, D.T.F. Utilization of Plant Genetic Resources: A Lifeboat to the Gene Pool. PhD Thesis, Department of Agriculture and Ecology, Faculty of Life Sciences, Copenhagen University, Denmark. ISBN: 978-91-628-8268-6. Available online at http://goo.gl/pYa9x, verified 21 Feb 2012.
  • Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community (TDWG, GBIF).
  • Berendsohn, W. and H. Knüpffer (2006). Draft mapping of Eurisco descriptors to ABCD 2.06. Available at http://www.bgbm.org/tdwg/codata/Schema/Mappings/EURISCO-2-ABCD.pdf, verified 21 Feb 2012.
  • Endresen, D., S. Gaiji, T. Robertson (2009). DarwinCore Germplasm Extension and deployment in the GBIF infrastructure. Proceedings of TDWG 2009, Montpellier, France. Bioversity Information Standards (TDWG). Available at http://www.tdwg.org/proceedings/article/view/464, verified 21 Feb 2012. Endresen, D.T.F. and H. Knüpffer (2011). The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets. p. 119-142. In: Endresen, D.T.F. Utilization of Plant Genetic Resources: A Lifeboat to the Gene Pool. PhD Thesis, Department of Agriculture and Ecology, Faculty of Life Sciences, Copenhagen University, Denmark. ISBN: 978-91-628-8268-6. Available online at http://goo.gl/pYa9x, verified 21 Feb 2012.
  • Darwin core
  • Hazekamp, T., J. Serwiski, and A. Alercia (1997). Appendix II. Multicrop passport descriptors (final version). p. 97-90. In: Lipman, E., M.W.M. Jongen, Th.J.L. van Hintum, T. Grass, and L. Maggioni (eds). Central crop databases: Tools for plant genetic resources management. International Plant Genetic Resources Institute (IPGRI), Rome, Italy/CGN, Wageningen, Netherlands. ISBN 92-9043- 320-5. 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
  • http://code.google.com/p/gbif-ecat/wiki/DwCArchive
  • GBIF Knowledge Organization System (KOS), http://kos.gbif.org/Prototype Vocabulary Wiki, http://kos.gbif.org/wiki/Prototype isoCAT Vocabulary management platform, http://kos.gbif.org/isocat/interface/TDWG Vocabulary Management Task Group (VoMaG), http://community.gbif.org/pg/groups/21382/vocabulary-management/GBIF Resources Registry, http://rs.gbif.org/ GBIF Resources Browser, http://tools.gbif.org/resource-browser/GBIF Vocabularies, http://vocabularies.gbif.org
  • GBIF Knowledge Organization System (KOS), http://kos.gbif.org/

Transcript

  • 1. Semantics for Biodiversity, May 16th – 18th 2012. Kansas University, Lawrence, KS. Dag Endresen, GBIF
  • 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. Potential of the GBIF technologyhttp://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 demoGenebank/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 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. 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. 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. 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 Serverhttp://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 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. http://community.gbif.org/pg/groups/21382/