Genebanks as GBIF data providers, the first experiences, at the TDWG 2004 conference
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Genebanks as GBIF data providers, the first experiences, at the TDWG 2004 conference

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Genebanks as GBIF data providers - the first experiences. Helmut Knüpffer and Norbert Biermann (IPK Gatersleben), Dag Endresen (Nordic Gene Bank), Pawel Kolasinski and Wieslaw Podyma (IHAR), Javier ...

Genebanks as GBIF data providers - the first experiences. Helmut Knüpffer and Norbert Biermann (IPK Gatersleben), Dag Endresen (Nordic Gene Bank), Pawel Kolasinski and Wieslaw Podyma (IHAR), Javier de la Torre (BGBM, ENBI). Presented at TDWG 2004 conference in Christchurch, New Zealand, 13 October 2004.

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  • You may change the order of authors (Dag Terje and Javier first) Also change the template – at present it is „too much IPK“ – you should also include the logos of NGB, BGBM, IHAR somewhere (I added them on the last slides) Please give my regards to the auditory Please make the presentation shorter – you have only 15 minutes, including discussion!!! Leave time for discussion.
  • Just to illustrate the way genebanks store their seeds
  • Just to illustrate the way genebanks store their seeds
  • More specifically, this is the „permanent garden“ – i.e. the place where perennial crops are planted for several years.
  • In addition to a herbarium (approx. 400,000 samples), IPK has more reference collections: Spike collection (for cereals) Seed collections (for many large-seeded crops, including legumes, cereals) Fruit collectons (in alcohol) Photographs, drawings
  • The COMECON descriptor list came earlier than Multi-Crop, it was the result of a cooperation of the Eastern European Genebanks in PGR documentation.
  • This is the complete list of Multi-Crop (in the EURISCO version) Descriptors marked red did not match earlier versions of ABCD
  • Dag Terje, maybe you have most up-to-date information about the number of accessions present in EURISCO
  • Here you can add screenshot(s) from the native NGB system, maybe the same accessions that will be shown in a (sequence of) screenshot(s) from GBIF (next slide) The same for IHAR (you can probably find the IHAR local database using GOOGLE and typing IHAR Radzikow or Radzików
  • Here you can add screenshot(s) from the native NGB system, maybe the same accessions that will be shown in a (sequence of) screenshot(s) from GBIF (next slide) The same for IHAR (you can probably find the IHAR local database using GOOGLE and typing IHAR Radzikow or Radzików
  • These two slides were taken from a presentation by Theo (from EPGRIS final meeting in Prague Sept 2003), they could quite well illustrate the EURISCO approach to the non-genetic-resources people at TDWG.
  • Same information as next page (table). If you can format the table more nicely, the first slide can be removed.

Genebanks as GBIF data providers, the first experiences, at the TDWG 2004 conference Presentation Transcript

  • 1. Genebanks as GBIF data providers the first experiences
    • Helmut Knüpffer, Norbert Biermann – IPK Gatersleben, Germany
    • Dag Terje Endresen – Nordic Gene Bank, Alnarp, Sweden
    • Pawel Kolasinski, Wieslaw Podyma – IHAR, Radzików, Poland
    • Javier de la Torre – BGBM, Berlin, Germany
    • TDWG 2004 – Christchurch, New Zealand
  • 2. TOPICS for this talk
    • Genebanks are biodiversity collections
    • Data exchange between genebanks
    • Central databases of plant genetic resources
    • Mapping of PGR descriptors to ABCD & Darwin Core
    • Linking genebanks to GBIF
    • Conclusions
  • 3. Genebanks as biodiversity collections (1)
    • Collections of crop plants, their wild relatives and other useful plants
    • Preserved as seeds, living plants, in vitro or cryo
    • Aims
      • provide plant material to breeders and researchers
      • counteract „genetic erosion“ by preserving threatened plants ex situ
  • 4. Genebanks as biodiversity collections (2)
    • Estimated: 6 million accessions in hundreds of genebanks worldwide, many well-documented
    • 6,100 (estimated 7,000) agricultural and horticultural crop plant species worldwide (excl. ornamentals & forest species) [Mansfeld]
    • >10,000 European wild species considered “crop wild relatives” [preliminary data PGR Forum]
    • Genebanks cover a large number of important taxa
    • Genebanks are a source for useful biodiversity and related information
  • 5. Genebanks as biodiversity collections (3)
    • Genebank tasks:
    • collection, acquisition
    • preservation
    • multiplication/rejuvenation
    • documentation
    • reference collections – herbaria, seed & spike samples, fruits)
    • distribution of plant genetic resources
  • 6. Genebanks Long-term seed storage (IPK)
  • 7. Genebanks Long-term seed storage (NGB)
  • 8. Genebanks Field multiplication
  • 9. Genebanks Reference collections, e.g. cereal spike & seed collection
  • 10. Data exchange between genebanks
    • Many genebanks have electronic documentation systems
    • PGR data exchange standards developed >30 years
      •  1988: “Passport descriptors of the COMECON International Database of Genetic Resources”
      •  1996: FAO/IPGRI „Multi-Crop Passport Descriptors“
      • 33 fields, fixed-format [resembles Darwin Core]
  • 11. Data exchange: Multi-Crop Passport Descriptors
    • 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]
  • 12. Central databases of plant genetic resources
    • 56 „ Central Crop Databases“ in Europe > 20 years (Wheat, Potato, Barley etc.)
    • EURISCO – central inventory of plant genetic resources in Europe
      • EU project EPGRIS (1999-2003)
      • 42 national programmes (Europe)
      • at present 906,824 accessions (approximately 50% of estimated number in European genebanks)
  • 13. Accessions in EURISCO (906,824)
  • 14. Accessions in SINGER (524,466)
  • 15. EURISCO - present situation (TvH) EURISCO database nat. inven-tory nat. inven-tory nat. inven-tory nat. inven-tory nat. inven-tory collection collection collection collection collection collection input collection collection collection collection output user user user user user user CCDB other sources
  • 16. The first genebanks in GBIF
    • Nordic Gene Bank (NGB), Alnarp, Sweden
      • 29,878 accessions, Darwin Core & DiGIR protocol, March 2004
    • IHAR Radzików, Poland
      • 40,459 accessions, Darwin Core & DiGIR protocol, March 2004
    • IPK Gatersleben, Germany
      • 109,711 accessions, ABCD & BioCASE protocol, August 2004 (assisted by ENBI)
  • 17. Conclusions
    • It is suggested that the PGR community utilizes the GBIF mechanisms and tools to build specific information services instead of their „central databases“
    • Specific portals should be built in the future to serve specific PGR communities, e.g.:
      • a „Barley Portal“ with barley genetic resources collections, but also herbaria and observations in the wild
  • 18.
    • Thank you for listening!