TDWG 2006, Missouri, U.S.A. Exchange of germplasm datasets with PyWrapper/BioCASE October 16, 2006 TDWG annual Meeting 2006 Missouri Botanical Garden St. Louis, Missouri, U.S.A. Dag Endresen, Nordic Gene Bank Johan Bäckman, Nordic Gene Bank Helmut Knüpffer, IPK Gatersleben Samy Gaiji, IPGRI, Bioversity International

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG TOPICS Genetic resources:  Data standards  Data exchange  Information network  Outlook

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Germplasm data, seed genebanks  Germplasm genebanks are biodiversity collections.  Collection level data Metadata about genebank institutes and the germplasm collections they hold.  Unit level data The unit level data for germplasm collections are the accessions. Genebank accessions share many properties and attributes with other biodiversity specimens.

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Germplasm Data Standards

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG IPGRI Crop Descriptors  The IPGRI crop descriptors are developed to standardize characterization and evaluation data – called “descriptive data” in TDWG context.  The MCPD (Multi Crop Passport Descriptors) is designed to standardize "passport data" across crops. It enables compatibility with the IPGRI crop specific descriptor lists and the FAO World Information and Early Warning System (WIEWS) and serves as a basis for data exchange.  The MCPD descriptor list was made fully compatible with ABCD 2.06

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Generation Challenge Programme, GCP_Passport_1.03 The Generation Challenge Programme is a research and capacity building network that uses plant genetic diversity to produce better crop varieties for resource-poor farmers. In the context of the GCP (Generation Challenge Programme), the GCP Passport data exchange schema was developed.

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG GCP_Passport Upgrade to ABCD

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG PGR sub-unit of ABCD 2.06

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Germplasm Data Catalogues

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Germplasm catalogues  Most genebank datasets are indexed by three major germplasm catalogues  EURISCO is the data catalogue of the European genebanks ( accessions)  SINGER is the portal to the international CGIAR collections ( accessions)  USDA-GRIN is the portal to the USDA ARS National Germplasm Repositories of the USA ( accessions)  All three catalogues are published in GBIF

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Data warehouse model

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Decentralized data network with web services

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Germplasm data exchange with PyWrapper/BioCASE  GBIF technology demonstrated to IPGRI, FAO, CGIAR centres and genebanks (2005) and widely adopted for PGR information networks  In the spring of 2004 the first European genebanks joined GBIF as data providers.  In 2005 USDA-GRIN joined GBIF.  In 2006 both SINGER and EURISCO joined GBIF.  The germplasm datasets worldwide are compatible with the MCPD data standard.  Sharing of germplasm datasets with GBIF was rather straight forward after mapping of the MCPD data standard to ABCD 2.06

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Germplasm BioCASE entry points [

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Decentralized model EURISCO (Data Portal Europe) Nordic Gene Bank (Northern Europe) IPK Gatersleben (Germany) IHAR (Poland) (Other European gene banks...) SINGER (Data Portal for CGIAR) (CGIAR International Future Harvest gene banks...) USDA GRIN (Data Portal USA) (USDA ARS National Germplasm Repositories...) WUR CGN (Netherlands) GBIF (Global Data Portal) USER chm.grinfo.net (Global germplasm Data Portal) Internet MCPD

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Germplasm data indexing  The genebanks are building data indexing methodologies for access to global germplasm data.  It is planned to build a “Clearing House Mechanism” for germplasm.  This data portal is developed in cooperation with GBIF, which is also harvesting global biodiversity data using a similar approach. [

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG  Global Unique Identifiers, GUID (LSID, Life Science Identifiers) [  Biodiversity informatics workflow tools (BioMOBY and Taverna) Work in progress

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Outlook  The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community.  Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.  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.  Users from the biodiversity community (who may not be aware of the existence of relevant material in genebanks) will find in GBIF genebank material of, e.g. crop wild relatives, along with data of the same species from herbaria, botanical gardens and floristic observations.

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Special thanks to  GBIF, Global Biodiversity Information Facility [  BioCASE, The Biological Collection Access Service for Europe. [  TDWG, Taxonomic Database Working Group [  GCP, The Generation Challenge Programme [

Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG Thanks for listening!