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GLOBAL BIODIVERSITY INFORMATION FACILITY TDWG 2009, Montpelier,  November 12, 2009 Dag Endresen (NordGen)  &  Samy Gaiji (GBIF) WWW.GBIF.ORG DarwinCore Germplasm Extension and deployment in the GBIF infrastructure
Topics for this session ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Darwin Core (2009) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
DwC star schema ,[object Object],[object Object]
DwC Germplasm Extension ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://www.nordgen.org/epgris3/wiki/index.php/DwC_Germplasm
DwC Germplasm Extension ,[object Object],[object Object],[object Object],[object Object]
DwC Germplasm (1)
DwC Germplasm (2)
DwC Germplasm (3)
DwC Germplasm (4)
DwC Germplasm (5)
DwC Germplasm (6) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Mapping of DwC-G terms  to the MCPD descriptors
Mapping of DwC-G terms  to the MCPD descriptors (continued)
MCPD -> ABCD 2.06 (2004) National Inventory Code Institute Code Accession Number Collecting Number Collecting Institute Code Genus Species Species Authority „ Subtaxa“ „ Subtaxa“ Authority Common Crop Name Accession Name Acquisition Date Country of Origin Location of Collection Site Latitude of CS Longitude of CS Elevation of CS Collecting Date of Sample Breeding Institute Code Biological Status of Accession Ancestral Data Collecting/Acquisition Source Donor Institute Code Donor Accession Number Other Identification (Number) associated with the accession Location of Safety Duplicates Type of Germplasm Storage Remarks Decoded Collecting Institute Decoded Breeding Institute Decoded Donor Institute Decoded Safety Duplication Location Accession URL Descriptors marked red did not match the earlier versions of ABCD    ABCD was extended by a PGR section [W. Berendsohn, H. Knüpffer] Helmut Knüpffer IPK Gatersleben Walter Berendsohn BGBM http://www.ecpgr.cgiar.org/epgris/Tech_papers/EURISCO_Descriptors.pdf
 
GBIF Informatics Suite ,[object Object],[object Object],[object Object]
IPT ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object]
GBIF Integrated Publishing Toolkit (IPT) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
http://ipt.nordgen.org/ipt/
IPT Interfaces ,[object Object],[object Object],[object Object],[object Object],[object Object]
Darwin Core Archive (DwC-A) ,[object Object],[object Object],[object Object],http://code.google.com/p/gbif-ecat/wiki/DwCArchive Germplasm.txt
The GBIF IPT service has a graphical interface to the datasets. Including a map, pie charts, or the right side context menu (taxonomy and geography).
The IPT user interface includes the extensions
XML interface includes the  extensions
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.
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).
GBIF PGR Network 2 http://data.gbif.org/datasets/network/2
Special thanks to: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Things can happen in a band, or any type of collaboration, that would not otherwise happen. (Jim Coleman, Musician)

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Darwin Core germplasm extension v 0.1, at TDWG 2009 conference (12 Nov 2009)

  • 1. GLOBAL BIODIVERSITY INFORMATION FACILITY TDWG 2009, Montpelier, November 12, 2009 Dag Endresen (NordGen) & Samy Gaiji (GBIF) WWW.GBIF.ORG DarwinCore Germplasm Extension and deployment in the GBIF infrastructure
  • 2.
  • 3.
  • 4.
  • 5.
  • 6.
  • 12.
  • 13. Mapping of DwC-G terms to the MCPD descriptors
  • 14. Mapping of DwC-G terms to the MCPD descriptors (continued)
  • 15. MCPD -> ABCD 2.06 (2004) National Inventory Code Institute Code Accession Number Collecting Number Collecting Institute Code Genus Species Species Authority „ Subtaxa“ „ Subtaxa“ Authority Common Crop Name Accession Name Acquisition Date Country of Origin Location of Collection Site Latitude of CS Longitude of CS Elevation of CS Collecting Date of Sample Breeding Institute Code Biological Status of Accession Ancestral Data Collecting/Acquisition Source Donor Institute Code Donor Accession Number Other Identification (Number) associated with the accession Location of Safety Duplicates Type of Germplasm Storage Remarks Decoded Collecting Institute Decoded Breeding Institute Decoded Donor Institute Decoded Safety Duplication Location Accession URL Descriptors marked red did not match the earlier versions of ABCD  ABCD was extended by a PGR section [W. Berendsohn, H. Knüpffer] Helmut Knüpffer IPK Gatersleben Walter Berendsohn BGBM http://www.ecpgr.cgiar.org/epgris/Tech_papers/EURISCO_Descriptors.pdf
  • 16.  
  • 17.
  • 18.
  • 19.
  • 20.
  • 22.
  • 23.
  • 24. The GBIF IPT service has a graphical interface to the datasets. Including a map, pie charts, or the right side context menu (taxonomy and geography).
  • 25. The IPT user interface includes the extensions
  • 26. XML interface includes the extensions
  • 27. 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.
  • 28. 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).
  • 29. GBIF PGR Network 2 http://data.gbif.org/datasets/network/2
  • 30.

Notas del editor

  1. Dublin Core : http://dublincore.org/ Darwin Core : http://rs.tdwg.org/dwc/
  2. Project site : http://rs.nordgen.org/dwc/ Wiki : http://www.nordgen.org/epgris3/wiki/index.php/DwC_Germplasm
  3. Project site : http://rs.nordgen.org/dwc/ Wiki : http://www.nordgen.org/epgris3/wiki/index.php/DwC_Germplasm
  4. Java: http://www.java.com/ Tomcat : http://tomcat.apache.org/ GeoServer : http://geoserver.org/ DarwinCore Archive (DwC-A) : http://www.gbif.org/informatics/standards-and-tools/publishing-data/data-standards/darwin-core-archives/ Hibernate : http://en.wikipedia.org/wiki/Hibernate_%28Java%29 H2 (DBMS) : http://en.wikipedia.org/wiki/H2_%28DBMS%29
  5. TAPIR (2004 ->) http://www.tdwg.org/standards/449/ ICIS (International Crop Information System): http://www.icis.cgiar.org BioMOBY (2001) http://biomoby.org , http://en.wikipedia.org/wiki/BioMOBY DiGIR (2002, not active) http://digir.sourceforge.net BioCASE (2003, PyWrapper v2) http://www.biocase.org EURISCO (2003, tab delimited text) http://eurisco.ecpgr.org PyWrapper 3 (2006, not active) http://trac.pywrapper.org TapirLink (2007) http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink GBIF Provider Toolkit (2009) http://code.google.com/p/gbif-providertoolkit
  6. http://code.google.com/p/gbif-ecat/wiki/DwCArchive
  7. http://ipt.nordgen.org/ipt/occResource.html?resource_id=45
  8. http://atlas.nordgen.org/rs/ipt/ipt_germplasm.xml http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm.xsd
  9. http://ipt.nordgen.org/ipt/occTaxon.html?resource_id=45&id=41799 http://ipt.nordgen.org/ipt/occDetail.html?guid=9099d7ce-8546-47d6-825b-eb599477dafd&resource_id=45 http://ipt.nordgen.org/ipt/occ/9099d7ce-8546-47d6-825b-eb599477dafd/xml
  10. Presentation of TDWG and GBIF 11/16/09
  11. Presentation of TDWG and GBIF 11/16/09 GBIF IPT: Markus Döring, Tim Robertson BioCASE and PyWrapper3 : Markus Döring, Javier de la Torre DiGIR and TapirLink software: Renato de Giovanni, Dave Vieglais