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Exchange of germplasm datasets with PyWrapper/BioCASE

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Dag Endresen, Nordic Gene Bank. Johan B ckman, Nordic Gene Bank. Helmut Kn pffer, IPK Gatersleben ... Exchange of germplasm datasets with PyWrapper/BioCASE, ... – PowerPoint PPT presentation

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Title: Exchange of germplasm datasets with PyWrapper/BioCASE


1
  • 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

2
TOPICS
  • Genetic resources
  • Data standards
  • Data exchange
  • Information network
  • Outlook

3
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.

4
  • Germplasm Data Standards

5
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

6
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.

7
GCP_Passport Upgrade to ABCD
8
PGR sub-unit of ABCD 2.06
9
  • Germplasm Data Catalogues

10
Germplasm catalogues
  • Most genebank datasets are indexed by three major
    germplasm catalogues
  • EURISCO is the data catalogue of the European
    genebanks (836 725 accessions)
  • SINGER is the portal to the international CGIAR
    collections (442 635 accessions)
  • USDA-GRIN is the portal to the USDA ARS National
    Germplasm Repositories of the USA (464 586
    accessions)
  • All three catalogues are published in GBIF

11
Data warehouse model
12
  • Decentralized data network with web services

13
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

14
Germplasm BioCASE entry points
http//chm.grinfo.net/index.php?appdata_provider
s
15
Decentralized model
chm.grinfo.net (Global germplasm Data Portal)
GBIF (Global Data Portal)
USER
(USDA ARS National Germplasm Repositories...)
USDA GRIN (Data Portal USA)
Internet
EURISCO (Data Portal Europe)
SINGER (Data Portal for CGIAR)
MCPD
(CGIAR International Future Harvest gene
banks...)
MCPD
MCPD
MCPD
MCPD
(Other European gene banks...)
Nordic Gene Bank (Northern Europe)
IPK Gatersleben (Germany)
WUR CGN (Netherlands)
IHAR (Poland)
16
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.
  • http//chm.grinfo.net

17
Work in progress
  • Global Unique Identifiers, GUID (LSID, Life
    Science Identifiers) http//lsid.sourceforge.net/
  • Biodiversity informatics workflow tools (BioMOBY
    and Taverna)

18
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.

19
Special thanks to
  • GBIF, Global Biodiversity Information Facility
    http//www.gbif.org
  • BioCASE, The Biological Collection Access Service
    for Europe. http//www.biocase.org
  • TDWG, Taxonomic Database Working Group
    http//www.tdwg.org
  • GCP, The Generation Challenge Programme
    http//www.generationcp.org/

20

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