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Status Seminar of the BMBF Programmes GBIF-Germany (GBIF-D) and BIOLOG-Biodiversity informatics

German version Deutsche Version

The Status Seminar offered a complete presentation of projects within the funding programme of the Federal Ministry of Education and Research. All 64 GBIF-D and 5 BIOLOG-AlgaTerra projects were summarized  in a status report and by posters. Apart from members of the Ministry's advisory board and other official representatives, more than 110 scientists, mainly collaborators in GBIF-D projects, attended the meeting.

  Vortrag

Oral presentations were organised in 4 sessions and gave a cross-project comprehensive overview, highlighting the programme's theme from various perspectives. The status report was published by PT-DLR und BGBM Berlin-Dahlem (ISBN 3-921800-53-6). The programme, status report, lectures and the list of posters are available as pdf files:

Programme pdf
Status Report 2004 (in English) pdf
Lectures (predominantly in German) pdf
List of posters (in English) pdf

Session I: Setting the stage

The participants were welcomed and the Status Seminar was introduced by Martin Rieland (BMBF, Bonn) and Walter Berendsohn (BGBM, Berlin).

James Edwards (GBIF Secretary) emphasized both the international context of GBIF Germany and the progress of the GBIF work programme for the last three years.  Currently, the GBIF Portal provides access to more than 45 million specimen-data records from 338 collections worldwide. James Edwards gave a broad overview of the aims in the near future and underscored the meaning of the German contributions and institutes to sustain international biodiversity research. Some of Germany´s contributions to GBIF:

  • Leader in standard development
  • Important contributor to NODES committee
  • Important data provider, including many images
  • Successful execution of projects co-financed by the Secretariat's seed money grants
  • Chair of Governing Board (Christoph Haeuser, SMNS Stuttgart)
  • Memberships in all GBIF committees and Science subcommittees

The presentation of Edmund Gittenberger (National Museum of Natural History Naturalis of the University Leiden) dealt with resources in the broadest sense (zoological record, voucher specimens und GenBank). His presentation focused on modern taxonomical methods (e.g. DNA sequencing), focussing on methodical developments in microbiology.

The German Node system, its meaning for German research and the priorities and management structure were presented in a discourse by the node co-ordinators group (Erko Stackebrandt, DSMZ Braunschweig; Christoph Häuser, SMNS Stuttgart; Dagmar Triebel, BSM München; Gerhard Haszprunar, ZSM München; Michael Türkay, FIS Frankfurt; Regine Jahn, BGBM Berlin; Renate van den Elzen, ZFMK Bonn; Walter Berendsohn, BGBM Berlin). 

Session II: Contribution to the IT-development

Buffet  

Alexandra Kehl (University Bayreuth) explained the co-ordination activities of the IT-Expert Group. The main objectives of the IT-Expert Group (homepage) include the documentation of IT-developments within the scope of biodiversity research and the co-ordination of workshops aiming at exchanging experience  and developing synergies.

Joachim Holstein (SMNS Stuttgart) compared the main collection management systems (SeSam, SysTax, Specify, DiversityWorkbench, DSMZ databank) in use within GBIF-Germany. All systems are contributing data to GBIF using the standards defined in the GBIF data architecture.

Gregor Hagedorn (Biologische Bundesanstalt für Land- und Forstwirtschaft, Berlin) explained available systems and concepts for the registration of none-molecular descriptions of organism and pointed out the meaning of descriptive data for biodiversity research.

Wolfgang Ludwig (Technische Universität München) described databank systems for DNA sequence data. The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.

Anton Güntsch (BGBM Berlin-Dahlem) presented technical details of the networking technology employed in GBIF (BioCASe protocol) und introduced the data definition ABCD (Access to Biological Collection Data), an XML-schema to describe biological collection information. ABCD and the BioCASe protocol are developed by international working groups co-ordinated in Germany. Both form part of the international GBIF data architecture.

Ekaterina Langer (Institute of Informatics, FU-Berlin) introduced the project „XML security mechanism for GBIF-Germany" for the conception und implementation of a security service for GBIF-D . The ongoing work focuses on the extension of the German GBIF-D architecture and system using XML security services to ensure confidentiality, integrity, authenticity and non-repudiation of data and message communication.

Session III: Application of freely available data in the net  

 

Gerhard Haszprunar (ZSM München) presented detailed information about nomenclatoral types and focused on their provision and uses in the Web environment. According to a DNFS report (German Director's Conference of Research Collections) the natural history collections in Germany, USA, GB and France are among the top 4 of the world. GBIF-D will mobilise a substantial amount of data for type specimens held in German collection: data will be captured for all vertebrate types, 10 % of the insect types, and 50-70% of other invertebrate type specimens.

  Poster

The lecture of Dagmar Fritze (DSMZ Braunschweig) addressed to accessions of  microbiological resources. The difference between the Prokaryotes Node and the other German Node is reflected in its role as a physical resource provider. Culture collection of microorganisms conserve the microbiological heritage and offer a genetically stable resource for scientists, institutes and the industry.

Martin Schnittler (University Greifswald), Frank Klingenstein (BfN Bonn) and Rudi May (BfN Bonn) accentuated the significance of freely available biodiversity data for the conservation of the natural environment. Biodiversity data can be used effectively for the compilation of red lists and distributions maps.

Robbert Gradstein (Albrecht-von-Haller-Institute Göttingen) emphasized the importance of access to biodiversity data for molecular research. He described the analysis of DNA extracts from herbarium and museum materials, which provide a historic and wide ranging source, although problems may be caused by inefficient drying, chemical preservation, and secondary ingredients). He gave hints for the optimisation of DNA extraction from herbarium- and museum collections.

The GBIF Species Bank is conceived as an archive for descriptive data which can close the gap between phylogenetical and descriptive taxonomy. In his presentation Thomas Friedl (Albrecht-von-Haller-Institute Göttingen) brought forward innovative views of using these data.

Christoph Häuser (SMNS Stuttgart) clarified the meaning of digital biodiversity information for international commitments and multilateral conventions, for example CBD - Convention on Biological Diversity, CITES  and Convention on Wetlands - Ramsar Convention.

Session IV: Perspectives

The Session IV focussed on the application and utilisation of primary biodiversity data for the solution of various scientific problems.

 

Marion Seier (CABI Bioscience, UK Centre) illustrated the potential utilisation of freely available primary biodiversity data to fight invasive species and explicated the biological control and approach of the international  project work of CABI Bioscience.

Buffet  

Invasive species are usually introduced and thrive in the absence of the predators of their natural environment. The classical biological control consists of the introduction of  co-evolved, host specific insects and pathogenes from native countries to confine the spread in the country of introduction. The availability of on-line databases of specimens (images!) and species information can  efficiently support  the fundamental research to initiate appropriate economical and ecological measures for biological control.

Marc Stadler (Bayer HealthCare) emphasized an utilisation of GBIF for the pre-selection of biological resources for industrial screening of natural material. Natural material in fungi has been successfully introduced in medical and pharmaceutical industries.  Many new active substances are primarily expected in fungi and marine invertebrates. Since the expenses of logistics and databank structures are very high, reliable taxonomical data via the internet can make pharmaceutical research more efficient by reducing the time needed in parts of the process, especially relating to the pre-selection of biological resources.

The final discussion  dealt with the co-operation of industry and research, GBIF´s assignments of priorities as well as the institutionalisation and consolidation of the successful set-up of Germany´s GBIF structure.

 

Outlook

 

Participants generally responded positively to the status seminar. It was made clear that research and industry has an increased demand for openly accessible on the Internet. The technical realisation of GBIF-D and the usability of GBIF information in several domain were demonstrated.

The representative of the Ministry stressed in his introduction that the GBIF-D programme of the BMBF has the purpose of providing start-up funding for the construction of the GBIF infrastructure in Germany. Long-term maintenance of the national GBIF system can only be accomplished by an institutionalisation of the tasks. This is the major challenge ahead for GBIF Germany. 

[Susanne Oehlschlaeger 12.01.2005]


Glossar

BGBM Botanischer Garten and Botanisches Museum Berlin-Dahlem, Freie Universität Berlin
BSM Botanische Staatssammlung München
CBD Convention on Biological Biodiversity
CITES Convention on International Trade on Endangered Species of Wild Fauna and Flora
DNFS Direktorenkonferenz naturwissenschaftlicher Forschungssammlungen Deutschlands
DSMZ Deutsche Sammlungen von Mikroorganismen und Zellkulturen GmbH, Braunschweig
FIS Forschungsinstitut Senckenberg Frankfurt a. M.
SMNS Staatliches Museum für Naturkunde Stuttgart
ZFMK Zoologisches Forschungsinstitut Museum A. Koenig, Bonn
ZSM Zoologische Staatssammlung München

 

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