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The Global Genome Biodiversity Network: Leveraging DNA and Tissue

collections globally

Gabi Dröge, Katharine Barker, Walter G. Berendsohn

Botanic Garden and Botanical Museum Berlin-Dahlem



Titelmasterformat durch Klicken bearbeitenGlobal Genome Biodiversity Network

• Network for non-human biobanks (e.g. DNA, tissue)

• Founded in 2011• Precursor project DNA Bank

Network founded in 2007 providing virtual infrastructure

• General secretariat: Smithsonian Institution

• Technical secretariat: Botanic Garden and Botanical Museum Berlin-Dahlem

• http://www.ggbn.org

http://www.ggbn.org/



Titelmasterformat durch Klicken bearbeitenGoals

• Data standard for sharing tissue and DNA information

• Portal to make biobank sample data available

• Institutional directory• Knowledge platform



Titelmasterformat durch Klicken bearbeitenGoals

• Best practices related to management and stewardship of genomic samples

• Recruit partners with different regional and taxonomic focus

• Identify gaps in GGBN collections



Titelmasterformat durch Klicken bearbeitenAudiences

• Biorepositories (contributors)• Organizations with living or

preserved specimens (contributors)

• Researchers (users)



Titelmasterformat durch Klicken bearbeitenToday: 37 GGBN members worldwide

6

http://www.humboldt.org.co/

http://www.nhm.ac.uk/

http://australianmuseum.net.au/

http://wiki.bgbm.org/dnabankwiki/index.php/File:Main_logo_DSMZ.jpg

http://wiki.bgbm.org/dnabankwiki/index.php/File:Logokoenig.gif



Titelmasterformat durch Klicken bearbeitenDeveloping Best Practices

• Recommendation for Biodiversity Biorepositories– Collaboration with ISBER*– April 2013, Submitted to ISBER – To be included into next version

of ISBER Best Practices• GGBN Document Library– Collaboration with ESBB**– May 2016, beta-release for

member use– Knowledge platform for non-

human biobanking

* International Society for Biological and Environmental Repositories** European, Middle Eastern and African Society for Biopreservation and Biobanking



Titelmasterformat durch Klicken bearbeitenDeveloping Best Practices

• Access and Benefit Sharing (ABS) compliance – July 2015, Documentation

available for member use• Material Transfer

Agreements• Code of Conduct• Statement of Use of

Genomic Material – Collaboration with

CETAF*– Provide trusted and

transparent access to genomic samples for users and contributors through an ABS framework

* Consortium of European Taxonomic Facilities



Titelmasterformat durch Klicken bearbeitenBusiness Model

• Will come into force 01/2016• Core and Associate members made a

commitment to become financial or in-kind contributors

• Current funding by:– German Research Foundation (DFG)– SYNTHESYS (EC)– In-kind contributions



Titelmasterformat durch Klicken bearbeitenBusiness Model: Pre-order samples in the Portal

• Order DNA or tissue samples through GGBN portal

• Download of sample information• Request forwarded to GGBN member

holding the sample(s)– Institution responsible for all further

steps• Checking availability and loaning conditions• Provide price offer to scientist• Request signing of Material Transfer

Agreement• Shipping samples

• Citation guidelines for samples coming soon (available at ggbn.org)




The GGBN Data Portal



Titelmasterformat durch Klicken bearbeitenGoal (December 2015): New Data Portal

• Expanded functionality

• Corporate Design• Based on feedback,

review and requirements of the GGBN community

• Public beta-release July 2015

http://data.ggbn.org/ggbn_new

• Final release December 2015






Titelmasterformat durch Klicken bearbeitenData Portal Architecture: Primary goal

Do not re-invent the wheel!




Source material / specimens Molecular analysis data

DNA & Tissue

Data Portal Architecture

http://www.ncbi.nlm.nih.gov/










Titelmasterformat durch Klicken bearbeitenPortal: Basic Architecture

Harvester(B-HIT)*

Data Cleaning

Index(MySQL

)

Store raw and cleaned data

Create SOLR index

Get full access toorginal record

Provider

IPT

Login, User settings

Query

*Berlin Harvesting and Indexing Toolkit

Provider

GBIF checklist

bank, CITES

External sources

GGBN web service



Titelmasterformat durch Klicken bearbeitenPortal: Taxonomic Backbone

Goals:• Query expansion: get synonyms and

accepted names• Keep names used by providersSources:• Certain datasets from GBIF checklist

bank web service– GBIF backbone, CoL, NCBI

• Prokaryotic Nomenclature up-to-date (PNU) web service

• EOL web service (under consideration)

• The Plant list web service (under consideration)



Titelmasterformat durch Klicken bearbeitenPortal: Aggregate data from multiple sources



Titelmasterformat durch Klicken bearbeitenPortal: Aggregate data from multiple sourcesExplore

Chenopodium ficifolium1908

specimens

42 nucleotide sequences

taxon page

3 DNA samples4 tissue samples

Getting live counts from other biodiversity portals for each record via web services




Titelmasterformat durch Klicken bearbeitenCITES @ GGBN

Warning and request for CITES registration number when ordering

the sample both for curator and user.



Titelmasterformat durch Klicken bearbeitenPortal: Statistics

Example: Samples from CaryophyllalesAbove: all records (DNA, tissue, specimens)Right: DNA / tissue samples



Titelmasterformat durch Klicken bearbeitenWhite Paper on Data Portal published

Droege et al. 2014



Titelmasterformat durch Klicken bearbeitenGGBN Data Standard

• http://terms.tdwg.org/wiki/GGBN_Data_Standard

• Based on ABCDDNA• Is meant to be used with ABCD or

DwC -> all occurrence terms are excluded (geography, scientificname etc.)

• Include elements of other standards (e.g. MIxS, SPREC)

• Collaboration with GBIF, Genomics Standards Consortium, GenBank, EMBL, ESBB, TDWG, and others

http://terms.tdwg.org/wiki/GGBN_Data_Standard







GGBN Data Standards





Vocabulary for - sample and

sequencing data- ABS- loan information






• Implementation for ABCD and Darwin Core-Archive available

• Supported by IPT (v2.2) and BioCASe (v3.5.3)– Tests performed by BGBM, NMNH,

CSIRO, ZFMK, DSMZ• Submission to TDWG as a standard in

12/2015• Submission to GSC* as a project in

08/2015

• Support provided by BGBM• White paper submitted

* Genomic Standards Consortium



Titelmasterformat durch Klicken bearbeitenUse Case: Environmental Samples and DNA• Environmental Samples already at

GGBN (bird fecal samples)–Works well with DwC-A and ABCD

• Environmental DNA at GGBN currently work in progress

Challenges:– Identification based on sequences– Hundreds of taxa– Proper search results and displaygenomic DNA (bird, plant) vs. environmental DNA (what bird has eaten) Users should find what they are looking for



Titelmasterformat durch Klicken bearbeitenUse Case: Environmental Samples and DNA

• Solution for ABCD: ABCDGGBN-Enviro• http://

data.ggbn.org/schemas/ggbn/Enviro/ABCDGGBN_Enviro.html

• GGBN extension @ Identification Sequences on identification level instead on unit level

http://data.ggbn.org/schemas/ggbn/Enviro/ABCDGGBN_Enviro.html





Titelmasterformat durch Klicken bearbeitenUse Case: Environmental Samples and DNA

• Solution for DwC-A: work in progress• Current star schema structure does

not allow 1:n:n relations• Collabortion with GBIF and GSC/MIxS

to find a solution




Join GGBN!



Titelmasterformat durch Klicken bearbeitenVouchers, traceability, deposition

Source: Droege et al. 2014

Every biodiversity biorepository is welcome to join GGBN.Researchers: deposit your samples and data in a GGBN collection if you don‘t have a DNA or tissue bank.GGBN provides a virtual and physical infrastructure to make your research traceable for the future.




go to http://data.ggbn.org to find available DNA from this specimen

Tracing back information



Titelmasterformat durch Klicken bearbeitenTracing back information



Titelmasterformat durch Klicken bearbeitenPortal: Number of Samples Online by Year

2009 2010 2011 2012 2013 2014 20150

20000

40000

60000

80000

100000

120000

140000

Samples Online



Titelmasterformat durch Klicken bearbeitenPortal: Number of Species Online by Year

2009 2010 2011 2012 2013 2014 20150

5000

10000

15000

20000

25000

Species Online



Titelmasterformat durch Klicken bearbeitenSecond GGBN International Conference21.-24. June

2016 Berlin



Titelmasterformat durch Klicken bearbeitenThank you

GGBN Interim Executive Committee

GGBN Members

GGBN Collaborators

GGBN Task Forces

DFG

SYNTHESYS

http://www.ggbn.org

[email protected]

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