Gabi Dröge, Katharine Barker, Walter G. Berendsohn

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1 Gabi Dröge, Katharine Barker, Walter G. Berendsohn
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

2 Global 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

3 Data standard for sharing tissue and DNA information
Goals Data standard for sharing tissue and DNA information Portal to make biobank sample data available Institutional directory Knowledge platform Gabi will expand on progress toward accomplishing the first goal, here I will outline progress on the other four goals. Emphasize task forces responsible.

4 Recruit partners with different regional and taxonomic focus
Goals Best practices related to management and stewardship of genomic samples Recruit partners with different regional and taxonomic focus Identify gaps in GGBN collections Gabi will expand on progress toward accomplishing the first goal, here I will outline progress on the other four goals. Emphasize task forces responsible.

5 Audiences Biorepositories (contributors) Organizations with living or preserved specimens (contributors) Researchers (users)

6 Today: 37 GGBN members worldwide

7 Developing 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

8 Developing 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

9 Business 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

10 Business 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)

11 The GGBN Data Portal

12 Goal (December 2015): New Data Portal
Expanded functionality Corporate Design Based on feedback, review and requirements of the GGBN community Public beta-release July 2015 Final release December 2015

13 Data Portal Architecture: Primary goal
Do not re-invent the wheel!

14 Data Portal Architecture
Molecular analysis data Source material / specimens DNA & Tissue

15 Portal: Basic Architecture
GBIF checklist bank, CITES IPT Provider Store raw and cleaned data Harvester (B-HIT)* Data Cleaning Index (MySQL) Provider Get full access to orginal record Create SOLR index External sources Query Login, User settings GGBN web service *Berlin Harvesting and Indexing Toolkit

16 Portal: Taxonomic Backbone
Goals: Query expansion: get synonyms and accepted names Keep names used by providers Sources: 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)

17 Portal: Aggregate data from multiple sources

18 Portal: Aggregate data from multiple sources
Explore Chenopodium ficifolium 1908 specimens 42 nucleotide sequences taxon page 3 DNA samples 4 tissue samples Getting live counts from other biodiversity portals for each record via web services

19 GGBN Warning and request for CITES registration number when ordering the sample both for curator and user.

20 Portal: Statistics Example: Samples from Caryophyllales
Above: all records (DNA, tissue, specimens) Right: DNA / tissue samples

21 White Paper on Data Portal published
Droege et al. 2014

22 GGBN 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

23 GGBN Data Standards

24 GGBN Data Standard Vocabulary for sample and sequencing data ABS
Vocabulary for sample and sequencing data ABS loan information

25 GGBN Data Standard 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

26 Use 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 display genomic DNA (bird, plant) vs. environmental DNA (what bird has eaten)  Users should find what they are looking for 

27 Use Case: Environmental Samples and DNA
Solution for ABCD: ABCDGGBN-Enviro GGBN Identification  Sequences on identification level instead on unit level

28 Use 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

29 Join GGBN!

30 Vouchers, 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.

31 Tracing back information
 go to to find available DNA from this specimen

32 Tracing back information

33 Tracing back information

34 Portal: Number of Samples Online by Year

35 Portal: Number of Species Online by Year

36 Second GGBN International Conference
June 2016 Berlin

37 Thank you http://www.ggbn.org ggbn@si.edu
GGBN Interim Executive Committee GGBN Members GGBN Collaborators GGBN Task Forces DFG SYNTHESYS