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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
Multiple data export services
                                 European
                                 Crop
                                 Databases



                                 European
    Genebank                     EURISCO
    dataset                      Catalog




                                Global Crop
                        GBIF    Registries




                                         4
2005 : BioCASE demo




Genebank/germplasm extension to the ABCD 2.06
                                                5
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
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
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
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
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.org/germplasm/ (in preparation)
    http://kos.gbif.org/wiki/Germplasm (wiki forum)               15
Darwin Core Archive (DwC-A)
   DwC-A publish dwc records including extensions
   Simple text based format
   Zipped single file archive




                         Germplasm.txt
Darwin Core Archive extension (XML)




 …

     http://rs.gbif.org/extension/nordgen/0.1/germplasm.xml
                                                              17
GBIF Vocabulary Server




http://vocabularies.gbif.org/node/163947


                                    18
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
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.
http://community.gbif.org/pg/groups/21382/

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Darwin Core extension for genebanks (germplasm), at Kansas University (May 2012)

  • 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
  • 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
  • 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.

Editor's Notes

  1. 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.
  2. 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).
  3. 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.
  4. 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.
  5. Darwin core
  6. 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
  7. http://code.google.com/p/gbif-ecat/wiki/DwCArchive
  8. 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
  9. GBIF Knowledge Organization System (KOS), http://kos.gbif.org/