Präsentation zum Thema: "Gabi Dröge, Katharine Barker, Walter G. Berendsohn"— Präsentation transkript:
1 Gabi Dröge, Katharine Barker, Walter G. Berendsohn The Global Genome Biodiversity Network: Leveraging DNA and Tissue collections globallyGabi Dröge, Katharine Barker, Walter G. BerendsohnBotanic Garden and Botanical Museum Berlin-Dahlem
2 Global Genome Biodiversity Network Network for non-human biobanks (e.g. DNA, tissue)Founded in 2011Precursor project DNA Bank Network founded in 2007 providing virtual infrastructureGeneral secretariat: Smithsonian InstitutionTechnical secretariat: Botanic Garden and Botanical Museum Berlin-Dahlem
3 Data standard for sharing tissue and DNA information GoalsData standard for sharing tissue and DNA informationPortal to make biobank sample data availableInstitutional directoryKnowledge platformGabi 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 GoalsBest practices related to management and stewardship of genomic samplesRecruit partners with different regional and taxonomic focusIdentify gaps in GGBN collectionsGabi will expand on progress toward accomplishing the first goal, here I will outline progress on the other four goals.Emphasize task forces responsible.
5 AudiencesBiorepositories (contributors)Organizations with living or preserved specimens (contributors)Researchers (users)
7 Developing Best Practices Recommendation for Biodiversity BiorepositoriesCollaboration with ISBER*April 2013, Submitted to ISBERTo be included into next version of ISBER Best PracticesGGBN Document LibraryCollaboration with ESBB**May 2016, beta-release for member useKnowledge 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) complianceJuly 2015, Documentation available for member useMaterial Transfer AgreementsCode of ConductStatement of Use of Genomic MaterialCollaboration 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 contributorsCurrent 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 portalDownload of sample informationRequest forwarded to GGBN member holding the sample(s)Institution responsible for all further stepsChecking availability and loaning conditionsProvide price offer to scientistRequest signing of Material Transfer AgreementShipping samplesCitation guidelines for samples coming soon (available at ggbn.org)
12 Goal (December 2015): New Data Portal Expanded functionalityCorporate DesignBased on feedback, review and requirements of the GGBN communityPublic beta-release July 2015Final release December 2015
13 Data Portal Architecture: Primary goal Do not re-invent the wheel!
14 Data Portal Architecture Molecular analysis dataSource material / specimensDNA & Tissue
15 Portal: Basic Architecture GBIF checklist bank, CITESIPTProviderStore raw and cleaned dataHarvester(B-HIT)*Data CleaningIndex(MySQL)ProviderGet full access toorginal recordCreate SOLR indexExternal sourcesQueryLogin, User settingsGGBN web service*Berlin Harvesting and Indexing Toolkit
16 Portal: Taxonomic Backbone Goals:Query expansion: get synonyms and accepted namesKeep names used by providersSources:Certain datasets from GBIF checklist bank web serviceGBIF backbone, CoL, NCBIProkaryotic Nomenclature up-to-date (PNU) web serviceEOL web service (under consideration)The Plant list web service (under consideration)
18 Portal: Aggregate data from multiple sources Explore Chenopodium ficifolium1908 specimens42 nucleotide sequencestaxon page3 DNA samples4 tissue samplesGetting live counts from other biodiversity portals for each record via web services
19 GGBNWarning 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 ABCDDNAIs 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
24 GGBN Data Standard Vocabulary for sample and sequencing data ABS Vocabulary forsample and sequencing dataABSloan information
25 GGBN Data StandardImplementation for ABCD and Darwin Core-Archive availableSupported by IPT (v2.2) and BioCASe (v3.5.3)Tests performed by BGBM, NMNH, CSIRO, ZFMK, DSMZSubmission to TDWG as a standard in 12/2015Submission to GSC* as a project in 08/2015Support provided by BGBMWhite 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 ABCDEnvironmental DNA at GGBN currently work in progressChallenges:Identification based on sequencesHundreds of taxaProper search results and displaygenomic 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-EnviroGGBN Identification Sequences on identification level instead on unit level
28 Use Case: Environmental Samples and DNA Solution for DwC-A: work in progressCurrent star schema structure does not allow 1:n:n relationsCollabortion with GBIF and GSC/MIxS to find a solution
30 Vouchers, traceability, deposition Source: Droege et al. 2014Every 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