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

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Presentation transcript:

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

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

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

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

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.

Where are the vouchers deposited? Both BGBM

Where are the vouchers deposited? BGBM SI

Verification of determination Digital voucher images whenever possible

Verification of determination Digital voucher images whenever possible

Verification of determination Digital voucher images whenever possible

External Vouchers Berlin DNA bank Where to find the data?

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

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

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

Associations Vision: All associated voucher data connected to DNA data

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

DNA parameters mandatory

On-demand extractions

Metadata, Citation format

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.

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?

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

Catalogue of Life Help to find the gaps

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