Visit to the NI Vavilov Institute for Plant Industry (VIR) in April 2010. Installation of the GBIF IPT toolkit for data publishing as a test upgrade for the EURISCO data infrastructure of European genebanks.
PPT: Nick King and Vishwas Chavan, Albuquerque, 2-7 Aug. 2009
EURISCO and GBIF IPT, at the Vavilov Institute in St Petersburg (27 April 2010)
Web service demo for EURISCO<br />GBIF Tools and Darwin Core extension for germplasm<br />N.I. Vavilov Research Institute of Plant Industry (VIR), April 26th – 29th 2010, St Petersburg, Russian Federation<br />Dag Endresen, Jonas Nordling, Nordic Genetic Resources Center (NordGen)<br />
Topics for this session<br /><ul><li>Web service installations for EURISCO
Possible Upgraded PGR Network Model<br /><ul><li>The gene bank dataset is shared from the holding gene bank.
The National Inventory (NI) endorse all national gene banks (and eventually individual accessions) for EURISCO.
ECPGR Crop databases can access passport data from EURISCO and additional crop specific data from the genebank IPT interface.
Standard data sharing tools ensure that the genebank dataset is available to other relevant decentralized thematic, regional or global networks.</li></ul>3<br />
Objectives of the EURISCO demo project<br /><ul><li>Evaluate the GBIF decentralized architecture
Install the IPT installation for 8 genebanks in Europe that, as far as possible, are also EURISCO/ECPGR partners.
Test the registration of IPT installation through the GBIF registry</li></ul> Global Biodiversity Resources Discovery System (GBRDS).<br /><ul><li>Test the Harvesting and Indexing Toolkit (HIT) installation for the EURISCO platform (Bioversity HQ, Rome).
Project runs until 20 December 2010.</li></ul>4<br />
2010 : IPT installations for EURISCO<br /><ul><li>EURISCO
Potential of the GBIF technology<br />Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.<br />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).<br />http://data.gbif.org/datasets/network/2<br />7<br />
Darwin Core<br />The purpose of DwC terms is to facilitate data sharing<br /><ul><li> a well-defined standard core vocabulary
a flexible framework to maximize re-usability </li></ul>The Darwin Core can be extended by adding new terms to share additional information.<br />Approved as TDWG standard 2009<br />“The Darwin Core is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information.”<br />http://rs.tdwg.org/dwc/<br />8<br />
DwC extension for germplasm<br />DwC Germplasm : DRAFT 0.1 : August 26, 2009<br /><ul><li> “MCPD in Darwin Core”
Additional terms to describe germplasm samples
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</li></ul>http://code.google.com/p/darwincore-germplasmhttp://rs.nordgen.org/dwc<br />9<br />
Mapping of DwC-G terms to the MCPD descriptors (EURISCO data exchange format)<br />10<br />
Mapping of DwC-G terms to the MCPD descriptors (continued)<br />11<br />
MCPD -> ABCD 2.06 (2004) for BioCASE<br />National Inventory Code<br />Institute Code<br />AccessionNumber<br />CollectingNumber<br />Collecting Institute Code<br />Genus<br />Species<br />SpeciesAuthority<br />„Subtaxa“<br />„Subtaxa“ Authority<br />Common Crop Name<br />Accession Name<br />Acquisition Date<br />Donor Institute Code<br />DonorAccessionNumber<br />OtherIdentification (Number) associatedwiththeaccession<br />Location of SafetyDuplicates<br />Type of Germplasm Storage<br />Remarks<br />DecodedCollecting Institute<br />DecodedBreeding Institute<br />DecodedDonor Institute<br />DecodedSafetyDuplicationLocation<br />Accession URL<br />Country of Origin<br />Location of Collection Site<br />Latitude of CS<br />Longitude of CS<br />Elevation of CS<br />Collecting Date of Sample<br />Breeding Institute Code<br />Biological Status of Accession<br />Ancestral Data<br />Collecting/AcquisitionSource<br />Helmut Knüpffer<br />IPK Gatersleben<br />http://www.ecpgr.cgiar.org/epgris/Tech_papers/EURISCO_Descriptors.pdf<br />Walter Berendsohn<br />BGBM<br />12<br />
GBIF Informatics Suite<br /><ul><li>GBIF tools to empower decentralized thematic or regional networks
Darwin Core extension for germplasm makes these tools usable for crop gene banks.</li></ul>13<br />
Integrated Publishing Toolkit (IPT)<br />A tool for data publishers.<br />A simple mechanism to share primary biodiversity data following the Darwin Core standard.<br />Open source, Java based web application.<br />Provides a local tool for data quality assessment, etc.<br />14<br />
Same dataset available from multiple information systems...<br />?!<br />VIR Crop <br />dataset<br />ECPGR Crop Databases<br />VIR (RUS001)<br />Passport data<br />EURISCO<br />Global Crop Registries<br />19<br />
Resolvable persistent identifiers can direct the user to the publisher of the primary dataset (official original dataset)<br />VIR Crop <br />dataset<br />ECPGR Crop Databases<br />VIR (RUS001)<br />Passport data<br />EURISCO<br />Global Crop Registries<br />20<br />
Persistent Identifier<br />The Persistent Identifier (PI) is a digital name tag<br />Also called Global Unique Identifiers (GUID)<br />Life Science Identifiers (LSID) is one example<br />Digital Object Identifier (doi) is another example<br />The Persistent Identifier concept for to naming and identification of data resources stored in multiple, distributed data stores.<br />Effective identification of data objects is essential for linking the world’s biodiversity data. <br />21<br />
Special thanks to:<br /><ul><li>GBIF, Global Biodiversity Information Facility http://www.gbif.org
TDWG, Biodiversity Information Standards http://www.tdwg.org
Bioversity International </li></ul>http://www.bioversityinternational.org<br />Things can happen in a band, or any type of collaboration, that would not otherwise happen. (Jim Coleman, Musician)<br />