Building the German DNA bank network using TDWG standards
Gabriele Dröge, Jörg Holetschek
Abstract
A DNA bank is a service facility for the long term storage of well documented DNA. For the German DNA bank network project, four partner institutions with complementary expertise and collections will form a pool: The Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM), the Bavarian State Collection of Zoology Munich (ZSM), the Forschungsmuseum Alexander König Bonn (ZFMK), and the German Collection of Microorganisms and Cell Cultures Braunschweig (DSMZ). The main focus of the network is to enhance taxonomic, systematic, genetic and evolutionary studies.
The BGBM is responsible for coordinating the establishment of the network, designing and implementing the network infrastructure, developing databases and the web portal, and storing botanical DNA samples (plants, algae, protists). Since October 2004, a DNA bank pilot project has been in progress at the BGBM, with researchers’ requests and shipping being processed continuously.
The architecture of the new network reflects the spread locations of natural history collections within Germany and aims at providing a central web portal for researchers to access data from various, distributed data sources. Each partner institution will have its own database for storing DNA data as well as the associated collection information. Most of the more recent DNA collections are stored in a variety of collection management systems, using either open standards software (e.g., Specify) or proprietary software. Whenever possible, integration of those data into the new system will be done by using BioCASe (Biological Collection Access Service).
In addition, a central web portal will be developed that can be used by researchers to explore the DNA material in stock at the partner institutions, view all of the associated information (metadata) as well as high-resolution digital images of the original specimens, and request DNA samples. Communication between the network components is based on the BioCASe protocol and ABCD and uses the BioCASe provider software as well as the Unitloader package for querying distributed data providers. In a later project phase, support for the TAPIR protocol will be implemented to make sure that collection providers following the latest protocol standards will be accessible.
By using protocol standards and standard software components the DNA Bank Network ensures that all data generated will be accessible to the international biodiversity data networking initiatives such as GBIF and BioCASE.
http://www.bgbm.org/bgbm/research/dna/
http://www.gbif.org
http://www.biocase.org
The BGBM is responsible for coordinating the establishment of the network, designing and implementing the network infrastructure, developing databases and the web portal, and storing botanical DNA samples (plants, algae, protists). Since October 2004, a DNA bank pilot project has been in progress at the BGBM, with researchers’ requests and shipping being processed continuously.
The architecture of the new network reflects the spread locations of natural history collections within Germany and aims at providing a central web portal for researchers to access data from various, distributed data sources. Each partner institution will have its own database for storing DNA data as well as the associated collection information. Most of the more recent DNA collections are stored in a variety of collection management systems, using either open standards software (e.g., Specify) or proprietary software. Whenever possible, integration of those data into the new system will be done by using BioCASe (Biological Collection Access Service).
In addition, a central web portal will be developed that can be used by researchers to explore the DNA material in stock at the partner institutions, view all of the associated information (metadata) as well as high-resolution digital images of the original specimens, and request DNA samples. Communication between the network components is based on the BioCASe protocol and ABCD and uses the BioCASe provider software as well as the Unitloader package for querying distributed data providers. In a later project phase, support for the TAPIR protocol will be implemented to make sure that collection providers following the latest protocol standards will be accessible.
By using protocol standards and standard software components the DNA Bank Network ensures that all data generated will be accessible to the international biodiversity data networking initiatives such as GBIF and BioCASE.
http://www.bgbm.org/bgbm/research/dna/
http://www.gbif.org
http://www.biocase.org