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The DNA Bank Network

The DNA Bank Network. Use Cases. Gabriele Droege. Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin. DNA Bank Network. German Collection of Microorganisms and Cell Cultures, Braunschweig Microorganisms. Botanic Garden and Botanical Museum Berlin-Dahlem

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The DNA Bank Network

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  1. The DNA Bank Network Use Cases Gabriele Droege Botanic Garden and Botanical Museum Berlin-Dahlem Freie Universität Berlin

  2. DNA Bank Network German Collection of Microorganisms and Cell Cultures, Braunschweig Microorganisms Botanic Garden and Botanical Museum Berlin-Dahlem Plants, algae and protists Coordination The New York Botanical Garden Plants Zool. Forschungsmuseum Alexander Koenig, Bonn Invertebrates and vertebrates Bavarian State Collection of Zoology, Munich Invertebrates and fungi Funding 2007-2011

  3. Goals • Deposition and Long-term storage of DNA samples and vouchers • Providing standardized access to DNA samples • Data infrastructure for reference purposes • Use of existing systems (e.g. GBIF, GenBank, CoL) • Partners work independent

  4. The Reference Problem Molecular analysis data Source material / specimens DNA Bank Network Webportal

  5. Search & Preorder

  6. Search & Preorder

  7. Search & Preorder Data Privacy Protection: Customer details recorded in index database and forwarded after finishing preorder. Shopping cart is deleted after finishing preorder. Shopping history is not recorded in index database! Every DNA bank receives its relevant order information only.

  8. Where are the vouchers deposited?  Both deposited @ BGBM

  9. Where are the vouchers deposited? • DNA @ BGBM • Specimen @ SI

  10. Verification of determination  Digital voucher images whenever possible

  11. Verification of determination  Digital voucher images whenever possible

  12. Verification of determination  Digital voucher images whenever possible

  13. External Vouchers Berlin DNA bank Where to find the data? 

  14. Where are the vouchers? No information about deposition of voucher and DNA sample available.  Requirement: Crosslinks between GenBank, GGBN and GBIF (all directions)

  15. Are there DNA samples or GenBank accessions? No information about further DNA samples/molecular analysis.  Requirement: Crosslinks between GBIF, GGBN and GenBank (all directions)

  16. Associations In situ voucher DNA Sample DNA voucher (cultivated plant) Tissue and Images from cultivated living plant

  17. Associations Vision: All associated voucher data connected to DNA data

  18. Associations Algae and sponge • Algae and Plant deposited in a herbarium but what about the animals and vice versa? • Collaboration with other DNA banks • Association of data Leaf miner and Plant

  19. DNA parameters mandatory

  20. On-demand extractions

  21. Metadata, Citation format

  22. Publications etc. • After ordering DNA the customers are asked by DNA bank curators to inform the relevant DNA bank about publications, GenBank accessions etc. related to orderêd DNA samples and follow the citation format (see Metadata).  Task for DNA bank curators not for the platform.

  23. Citations of DNA and vouchers Vision: All available publications related to a single DNA or voucher connected to our data Following the DSMZ example.  How can GGBN help?

  24. Reports • Record every search key and resulting hits in database • Web statistics -> what are people looking for? -> what search key often results in “no hits”  help to find gaps

  25. Catalogue of Life  Help to find the gaps

  26. Collection Management • Open source software for specimen and/or DNA data management • list of recommendations

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