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Germplasm data exchange, CGIAR SINGER (2009)

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CGIAR SINGER planning meeting on network infrastructure. At USDA GRIN, Washington, 25th August 2009. Dag Endresen (Bioversity/NordGen)

CGIAR SINGER planning meeting on network infrastructure. At USDA GRIN, Washington, 25th August 2009. Dag Endresen (Bioversity/NordGen)

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  • IMAGE: http://blog.tapirtype.com/cartoons/ [Creative Commons License: http://creativecommons.org/licenses/by-nc-sa/3.0/us/]
  • TAPIR(2004 ->) http://www.tdwg.org/standards/449/ICIS (International Crop Information System): http://www.icis.cgiar.orgBioMOBY (2001)http://biomoby.org, http://en.wikipedia.org/wiki/BioMOBYDiGIR (2002, not active)http://digir.sourceforge.netBioCASE (2003, PyWrapper v2)http://www.biocase.orgEURISCO (2003, tab delimited text)http://eurisco.ecpgr.orgPyWrapper 3 (2006, not active)http://trac.pywrapper.orgTapirLink (2007)http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLinkGBIF Provider Toolkit (2009)http://code.google.com/p/gbif-providertoolkit
  • http://ipt.nordgen.org/ipt/occResource.html?resource_id=45
  • http://ipt.nordgen.org/ipt/occTaxon.html?resource_id=45&id=41799http://ipt.nordgen.org/ipt/occDetail.html?guid=9099d7ce-8546-47d6-825b-eb599477dafd&resource_id=45http://ipt.nordgen.org/ipt/occ/9099d7ce-8546-47d6-825b-eb599477dafd/xml
  • http://atlas.nordgen.org/rs/ipt/ipt_germplasm.xmlhttp://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm.xsd
  • http://en.wikipedia.org/wiki/Darwin_Corehttp://rs.tdwg.org/dwc/terms/index.htmhttp://code.google.com/p/darwincore/http://code.google.com/p/darwincore/source/browse/#svn/trunk/xsd/profiles/germplasm
  • Transcript

    • 1. Data exchange alternatives
      GBIF Tools and Darwin Core germplasm extension
      Cartoon by Sasha Kopf (Creative Commons)
      SINGER GPG2 Consultation Meeting, USDA, Washington DC
      Dag Terje Filip Endresen, Nordic Genetic Resources Center, NordGen (Sweden)
    • 2. GBIF IPT
      Home: http://code.google.com/p/gbif-providertoolkit/
      Primary developers: Markus Döring, Tim Robertson
      Source code: Java Released: 2009
      Alternatives:
      -------
      • TAPIR (2004 ->)
      -------
      • DiGIR(PHP, 2001-2006)
      • 3. TapirLink(PHP, 2007 ->)
      -------
      • BioCASE(Python, 2001-2008)
      • 4. PyWrapper3 (Python, 2006-2008)
      -------
      • EURISCO (tab-delimited, 2003)
      -------
      • ICIS (Java, 1996 ->)
      -------
      • BioMOBY(Perl, 2001 ->)
      DEMO at http://ipt.nordgen.org/ipt/
      2
    • 5. GBIF IPT
      The GBIF IPT service comes with a graphical interface to explore the datasets published.
      The visitor may explore the dataset from the map, different pie charts, or the right side context menu (taxonomy and geography).
      3
    • 6. IPT
      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 (GBIF, TDWG).
      4
    • 7. GBIF IPT
      GBIF IPT implements the Darwin Core Standard; and provides an interface to easily build extensions to the core Darwin Core terms.
      The draft germplasm extension is one example of how-to extend the Darwin Core terms for the GBIF IPT.
      http://atlas.nordgen.org/rs/ipt/ipt_germplasm.xml
      http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm.xsd
      5
    • 8. Darwin Core
      A new version of Darwin Core is up for public review.
      http://rs.tdwg.org/dwc/terms/index.htm
      TDWG 2009, Montpellier, November 9 -13
      DRAFT Germplasm extension
      http://code.google.com/p/darwincore/source/browse/#svn/trunk/xsd/profiles/germplasm
      Please consider to contribute!
      RDF, LSID, ontology friendly
      6
    • 9. GBIF PGR Network 2
      PGR GBIF network
      Use of GBIF technology and integration of PGR collection data into GBIF allows PGR users to simultaneously search PGR collections and other biodiversity collections, and to get access to the data (and possibly the material) of relevant biodiversity collections.
      [http://data.gbif.org/datasets/network/2]
      7
    • 10. GBIF GBRDS
      http://gbrds.gbif.org
      8
      Slide prepared by GBIF (SamyGaiji)
    • 11. GBIF GBRDS
      http://gbrds.gbif.org
      9
      Slide prepared by GBIF (SamyGaiji)
    • 12. GBIF IPT
      • The GBIF IPT is an open source, Java (TM) based web application that connects and serves primary biodiversity data.
      • 13. The data registered in the IPT is connected to the GBIF distributed network and made available for public access.
      • 14. Designed to decentralize and speed up the process of indexing (large) biodiversity occurrence datasets.
      • 15. IPT also provides a local tool for data quality assessment to data publishers.
      • 16. The data publisher can easily monitor data access and use.
      10
    • 17. Special thanks to
      • GBIF, Global Biodiversity Information Facility http://www.gbif.org
      • 18. TDWG, Biodiversity Information Standards http://www.tdwg.org
      • 19. BioCASE, The Biological Collection Access Service for Europe.
      http://www.biocase.org
      • Bioversity International
      http://www.bioversityinternational.org
      Things can happen in a band, or any type of collaboration, that would not otherwise happen. (Jim Coleman, Musician)
      11

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