the dna bank network use cases gabriele droege botanic garden and botanical museum berlin-dahlem...
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The DNA Bank NetworkUse 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 2007-2011
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
Search & Preorder
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 deposited @ BGBM
Where are the vouchers deposited?
DNA @ BGBM
Specimen @ 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 parametersm
andato
ry
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