the dna bank network use cases gabriele droege botanic garden and botanical museum berlin-dahlem...

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