GLOBALBIODIVERSITYGLOBALBIODIVERSITYINFORMATIONFACILITYINFORMATIONFACILITY

TDWG 2009, Montpelier, TDWG 2009, Montpelier, November November 12, 200912, 2009Dag Endresen (NordGen)Dag Endresen (NordGen) & Samy Gaiji Samy Gaiji (GBIF)(GBIF)

WWW.GBIF.ORG

WWW.GBIF.ORG

DarwinCore Germplasm Extension DarwinCore Germplasm Extension and deployment in the GBIF and deployment in the GBIF

infrastructureinfrastructure

DarwinCore Germplasm Extension DarwinCore Germplasm Extension and deployment in the GBIF and deployment in the GBIF

infrastructureinfrastructure

Topics for this sessionTopics for this session

Darwin Core (2009) DwC Germplasm Extension (DRAFT 0.1) Germplasm Extension Terms Mapping to the Multi-Crop Passport

Descriptors Integrated Publishing Toolkit (IPT) IPT Germplasm Extension

Darwin Core (2009)Darwin Core (2009)

The Darwin Core should be viewed as an extension of the Dublin Core for biodiversity information.

The purpose of these terms is to facilitate data sharing a well-defined standard core

vocabulary a flexible framework to maximize re-usability

The Darwin Core can be extended by adding new terms to share additional information.

http://rs.tdwg.org/dwc/

DwC star schemaDwC star schema

Star schema model

Can relate elements one-to-many

DwC Germplasm ExtensionDwC Germplasm Extension

DwC Germplasm Extension (DRAFT 0.1) August 26, 2009

The DarwinCore Germplasm Extension additional terms to describe germplasm samples maintained by genebanks

worldwide

http://rs.nordgen.org/dwc/

http://www.nordgen.org/epgris3/wiki/index.php/DwC_Germplasm

DwC Germplasm ExtensionDwC Germplasm Extension

DwC Germplasm Extension (DRAFT 0.1)

Modelled starting from the Multi-Crop Passport standard (MCPD, 2001)

Includes the new terms for crop trait experiments developed as part of the European EPGRIS3 project.

Includes a few additional terms for new international crop treaty regulations.

DwC Germplasm (1)DwC Germplasm (1)

DwC Germplasm (2)DwC Germplasm (2)

DwC Germplasm (3)DwC Germplasm (3)

DwC Germplasm (4)DwC Germplasm (4)

DwC Germplasm (5)DwC Germplasm (5)

DwC Germplasm (6)DwC Germplasm (6)

GermplasmDistributionPerhaps add new terms to facilitate the reporting of germplasm distribution for the ITPGRFA (International Treaty for Genetic Resources for Food and Agriculture)

GermplasmManagementThe Millennium Seed Bank (Kew) has contributed feedback to the DwC-G modeling and proposed to include a number of seed management descriptors.

• Seed processing terms• Seed cleaning• Seed germination testing

Mapping of DwC-G terms to the MCPD descriptors

Mapping of DwC-G terms to the MCPD descriptors

Mapping of DwC-G terms to the MCPD descriptors (continued)

Mapping of DwC-G terms to the MCPD descriptors (continued)

MCPD -> ABCD 2.06 (2004)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 NameAccession NameAcquisition Date

Country of OriginLocation of Collection SiteLatitude of CSLongitude of CSElevation of CSCollecting Date of SampleBreeding Institute CodeBiological Status of

AccessionAncestral DataCollecting/Acquisition

Source

Donor Institute CodeDonor Accession NumberOther Identification (Number)

associated with the accession

Location of Safety DuplicatesType of Germplasm StorageRemarksDecoded Collecting InstituteDecoded Breeding InstituteDecoded Donor InstituteDecoded Safety Duplication

LocationAccession URL

Descriptors marked red did not match the earlier versions of ABCD ABCD was extended by a PGR section [W. Berendsohn, H. Knüpffer]

Helmut KnüpfferIPK Gatersleben

Walter BerendsohnBGBM

http://www.ecpgr.cgiar.org/epgris/Tech_papers/EURISCO_Descriptors.pdf

GBIF Informatics SuiteGBIF Informatics Suite

GBIF Decentralization Strategy (WP 2009-2010)

Customized biodiversity data networks

Tools to empower decentralized thematic or regional networks

IPTIPT

Project site: http://code.google.com/p/gbif-providertoolkit/

IPT DEMO. http://ipt.gbif.org/ IPT LITE DEMO: http://ipt-lite.gbif.org/index.html IPT Mailing List: http://lists.gbif.org/mailman/listinfo/ipt/

GBIF HIT: http://code.google.com/p/gbif-indexingtoolkit/ GBRDS: http://code.google.com/p/gbif-registry/

• The GBIF IPT is an open source, Java (TM) based web application that connects and serves primary biodiversity data.

• The data registered in the IPT is connected to the GBIF distributed network and made available for public access.

• Designed to decentralize and speed up the process of indexing (large) biodiversity occurrence datasets.

• IPT also provides a local tool for data quality assessment to data publishers.

GBIF Integrated Publishing Toolkit (IPT)GBIF Integrated Publishing Toolkit (IPT)

- Java 1.5 or higher is required- Apache Tomcat is recommended (1 GB

RAM+)- GBIF IPT is provided as a WAR archive (for

easy deployment)- GeoServer is included for web mapping

(OGC Compliant, WFS, WMS, etc)- H2 Embedded Java Database (with JDBC

interface and web console)- Hibernate (object relational mapping)

http://ipt.nordgen.org/ipt/

IPT InterfacesIPT Interfaces

REST XML TAPIR DwC Archive OGC (WFS, WMS, Web

Mapping) EML (Ecological Markup

Language)

Darwin Core Archive (DwC-A)Darwin Core Archive (DwC-A)

DwC-A publish dwc records including extensions Simple text based format Zipped single file archive

Germplasm.txt

http://code.google.com/p/gbif-ecat/wiki/DwCArchive

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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

The IPT user interface includes the extensions

XML 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 2GBIF PGR Network 2

http://data.gbif.org/datasets/network/2

• GBIF, Global Biodiversity Information Facility http://www.gbif.org

• TDWG, Biodiversity Information Standards http://www.tdwg.org

• 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)

Special thanks to:Special thanks to: